diff --git a/internal/sync/reference/defensive_test.go b/internal/sync/reference/defensive_test.go
index 064511af..8ae4bcaf 100644
--- a/internal/sync/reference/defensive_test.go
+++ b/internal/sync/reference/defensive_test.go
@@ -33,3 +33,11 @@ func TestStructuredAdaptersRejectMalformedSources(t *testing.T) {
 		})
 	}
 }
+
+func TestMarkdownProfilesRejectUnsafeMarkers(t *testing.T) {
+	_, err := parseMarkdownProfile(
+		Document{Path: "instructions.md", Data: []byte("<!-- launchdarkly:begin one -->\n")},
+		false,
+	)
+	require.Error(t, err)
+}
diff --git a/internal/sync/reference/profile_test.go b/internal/sync/reference/profile_test.go
new file mode 100644
index 00000000..734af835
--- /dev/null
+++ b/internal/sync/reference/profile_test.go
@@ -0,0 +1,81 @@
+package reference
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	syncdomain "github.com/launchdarkly/ldcli/internal/sync"
+)
+
+func TestMarkdownProfilesPreserveActivationMetadata(t *testing.T) {
+	tests := []struct {
+		name, fixture, realPath, format, metadataPath string
+		metadataValue                                 any
+	}{
+		{name: "Cursor", fixture: "profiles/cursor-rule.mdc", realPath: ".cursor/rules/support.mdc", format: "cursor", metadataPath: "frontmatter.globs", metadataValue: "src/support/**/*.ts"},
+		{name: "Copilot", fixture: "profiles/copilot.instructions.md", realPath: ".github/instructions/support.instructions.md", format: "copilot", metadataPath: "frontmatter.applyTo", metadataValue: "src/support/**/*.ts"},
+		{name: "Claude", fixture: "profiles/claude-instructions.md.golden", realPath: "CLAUDE.md", format: "claude-markdown", metadataPath: "frontmatter.model", metadataValue: "sonnet"},
+	}
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			documentPath, source := materializeFixture(t, test.fixture, test.realPath)
+			id := syncdomain.VariationID("project", "config", "default")
+			reference := syncdomain.Reference{File: documentPath, Format: test.format}
+			root, err := parseSourceDocument(Document{Path: documentPath, Data: source}, test.format)
+			require.NoError(t, err)
+			metadata, err := resolveSourcePath(root, test.metadataPath)
+			require.NoError(t, err)
+			assert.Equal(t, test.metadataValue, metadata.value)
+
+			projection, err := ParseSource(sourceBundle(documentPath, source), id, syncdomain.VariationModeAgent, reference)
+			require.NoError(t, err)
+			prompt := "Updated profile instructions."
+			result, err := UpdateSource(
+				sourceBundle(documentPath, source), id, syncdomain.VariationModeAgent, reference,
+				syncdomain.VariationProjection{Mode: syncdomain.VariationModeAgent, Instructions: &prompt},
+			)
+			require.NoError(t, err)
+			updated := applyConformanceEdits(t, source, directEdits(t, result))
+			root, err = parseSourceDocument(Document{Path: documentPath, Data: updated}, test.format)
+			require.NoError(t, err)
+			metadata, err = resolveSourcePath(root, test.metadataPath)
+			require.NoError(t, err)
+			assert.Equal(t, test.metadataValue, metadata.value)
+			assert.NotNil(t, projection)
+		})
+	}
+}
+
+func TestAgentsMarkdownSectionsAndMarkers(t *testing.T) {
+	documentPath, source := materializeFixture(t, "profiles/agents-instructions.md.golden", "AGENTS.md")
+	id := syncdomain.VariationID("project", "config", "default")
+	tests := []struct {
+		name, selectPath, mapPath, want string
+	}{
+		{name: "section", selectPath: `sections[heading="Support"]`, mapPath: "body", want: "Ask for an order ID.\n\n<!-- launchdarkly:begin refunds -->\nExplain the refund policy.\n<!-- launchdarkly:end refunds -->"},
+		{name: "marker", selectPath: `markers[id="refunds"]`, mapPath: "body", want: "Explain the refund policy."},
+	}
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			reference := syncdomain.Reference{
+				File: documentPath, Format: "agents-markdown", Select: test.selectPath,
+				Map: map[string]string{"prompt": test.mapPath},
+			}
+			projection, err := ParseSource(
+				sourceBundle(reference.File, source), id, syncdomain.VariationModeAgent, reference,
+			)
+			require.NoError(t, err)
+			assert.Equal(t, test.want, *projection.(syncdomain.VariationProjection).Instructions)
+			prompt := "Updated selected instructions."
+			result, err := UpdateSource(
+				sourceBundle(reference.File, source), id, syncdomain.VariationModeAgent, reference,
+				syncdomain.VariationProjection{Mode: syncdomain.VariationModeAgent, Instructions: &prompt},
+			)
+			require.NoError(t, err)
+			updated := applyConformanceEdits(t, source, directEdits(t, result))
+			assert.Contains(t, string(updated), "## Build\n\nRun `make test`.")
+		})
+	}
+}
diff --git a/internal/sync/reference/profiles.go b/internal/sync/reference/profiles.go
new file mode 100644
index 00000000..68aeb103
--- /dev/null
+++ b/internal/sync/reference/profiles.go
@@ -0,0 +1,126 @@
+package reference
+
+import (
+	"bytes"
+	"fmt"
+	"strings"
+
+	"gopkg.in/yaml.v3"
+
+	syncdomain "github.com/launchdarkly/ldcli/internal/sync"
+)
+
+type markdownProfileAdapter struct {
+	format      string
+	frontMatter bool
+}
+
+func (adapter markdownProfileAdapter) Format() string { return adapter.format }
+func (adapter markdownProfileAdapter) Inspect(bundle SourceBundle) (Inspection, error) {
+	root, err := parseMarkdownProfile(bundle.Primary, adapter.frontMatter)
+	return Inspection{root: root}, err
+}
+func (markdownProfileAdapter) Defaults(kind syncdomain.Kind) (string, map[string]string) {
+	if kind == syncdomain.KindVariation {
+		return "$", map[string]string{string(syncdomain.FieldPrompt): "body"}
+	}
+	return "$", nil
+}
+
+func init() {
+	mustRegister(markdownProfileAdapter{format: "cursor", frontMatter: true})
+	mustRegister(markdownProfileAdapter{format: "copilot", frontMatter: true})
+	mustRegister(markdownProfileAdapter{format: "agents-markdown"})
+	mustRegister(markdownProfileAdapter{format: "claude-markdown", frontMatter: true})
+}
+
+func parseMarkdownProfile(document Document, supportsFrontMatter bool) (*sourceNode, error) {
+	data := document.Data
+	bodyStart := 0
+	frontmatter := &sourceNode{value: map[string]any{}, fields: map[string]*sourceNode{}}
+	trimmed := bytes.TrimPrefix(data, []byte("\ufeff"))
+	bomLength := len(data) - len(trimmed)
+	if supportsFrontMatter && bytes.HasPrefix(trimmed, []byte("---")) {
+		region, start, err := splitFrontMatter(data)
+		if err != nil {
+			return nil, err
+		}
+		bodyStart = start
+		var documentNode yaml.Node
+		if err := yaml.Unmarshal(region.data, &documentNode); err != nil {
+			return nil, fmt.Errorf("invalid profile front matter: %w", err)
+		}
+		if len(documentNode.Content) != 0 {
+			frontmatter, err = yamlSourceNode(region.data, documentNode.Content[0], region.startOffset)
+			if err != nil {
+				return nil, err
+			}
+		}
+	} else {
+		bodyStart = bomLength
+	}
+	bodyData := data[bodyStart:]
+	body := markdownTextNode(bodyData, bodyStart, len(data))
+	sections := &sourceNode{items: markdownSections(bodyData), collection: true}
+	offsetSourceSpans(sections, bodyStart)
+	markers, err := markdownMarkers(bodyData, bodyStart)
+	if err != nil {
+		return nil, err
+	}
+	return &sourceNode{fields: map[string]*sourceNode{
+		"frontmatter": frontmatter,
+		"body":        body,
+		"sections":    sections,
+		"markers":     markers,
+	}}, nil
+}
+
+func markdownMarkers(data []byte, base int) (*sourceNode, error) {
+	const beginPrefix = "<!-- launchdarkly:begin "
+	const endPrefix = "<!-- launchdarkly:end "
+	var items []*sourceNode
+	openID, bodyStart := "", 0
+	for offset := 0; offset < len(data); {
+		lineEnd := nextLineEnd(data, offset)
+		line := strings.TrimSpace(string(data[offset:lineEnd]))
+		switch {
+		case strings.HasPrefix(line, beginPrefix) && strings.HasSuffix(line, "-->"):
+			if openID != "" {
+				return nil, fmt.Errorf("nested LaunchDarkly marker %q", openID)
+			}
+			openID = strings.TrimSpace(strings.TrimSuffix(strings.TrimPrefix(line, beginPrefix), "-->"))
+			bodyStart = lineEnd
+		case strings.HasPrefix(line, endPrefix) && strings.HasSuffix(line, "-->"):
+			id := strings.TrimSpace(strings.TrimSuffix(strings.TrimPrefix(line, endPrefix), "-->"))
+			if openID == "" || id != openID {
+				return nil, fmt.Errorf("LaunchDarkly marker %q has no matching begin marker", id)
+			}
+			body := markdownTextNode(data[bodyStart:offset], base+bodyStart, base+offset)
+			items = append(items, &sourceNode{fields: map[string]*sourceNode{
+				"id": {value: id}, "body": body,
+			}})
+			openID = ""
+		}
+		offset = lineEnd
+	}
+	if openID != "" {
+		return nil, fmt.Errorf("LaunchDarkly marker %q is not closed", openID)
+	}
+	return &sourceNode{items: items, collection: true}, nil
+}
+
+func offsetSourceSpans(node *sourceNode, offset int) {
+	if node == nil {
+		return
+	}
+	if node.start != 0 || node.end != 0 {
+		node.start += offset
+		node.end += offset
+	}
+	for _, child := range node.fields {
+		offsetSourceSpans(child, offset)
+	}
+	for _, child := range node.items {
+		offsetSourceSpans(child, offset)
+	}
+}
diff --git a/internal/sync/reference/testdata/profiles/agents-instructions.md.golden b/internal/sync/reference/testdata/profiles/agents-instructions.md.golden
new file mode 100644
index 00000000..28d9f467
--- /dev/null
+++ b/internal/sync/reference/testdata/profiles/agents-instructions.md.golden
@@ -0,0 +1,13 @@
+# Repository guide
+
+## Support
+
+Ask for an order ID.
+
+<!-- launchdarkly:begin refunds -->
+Explain the refund policy.
+<!-- launchdarkly:end refunds -->
+
+## Build
+
+Run `make test`.
diff --git a/internal/sync/reference/testdata/profiles/claude-instructions.md.golden b/internal/sync/reference/testdata/profiles/claude-instructions.md.golden
new file mode 100644
index 00000000..f4a10263
--- /dev/null
+++ b/internal/sync/reference/testdata/profiles/claude-instructions.md.golden
@@ -0,0 +1,10 @@
+---
+name: support
+description: Support subagent instructions
+tools: Read, Grep
+model: sonnet
+---
+
+# Support subagent
+
+Ask for an order ID and follow the support policy.
diff --git a/internal/sync/reference/testdata/profiles/copilot.instructions.md b/internal/sync/reference/testdata/profiles/copilot.instructions.md
new file mode 100644
index 00000000..024f8f36
--- /dev/null
+++ b/internal/sync/reference/testdata/profiles/copilot.instructions.md
@@ -0,0 +1,7 @@
+---
+applyTo: "src/support/**/*.ts"
+---
+
+# Support
+
+Use the support policy.
diff --git a/internal/sync/reference/testdata/profiles/cursor-rule.mdc b/internal/sync/reference/testdata/profiles/cursor-rule.mdc
new file mode 100644
index 00000000..6eef5da2
--- /dev/null
+++ b/internal/sync/reference/testdata/profiles/cursor-rule.mdc
@@ -0,0 +1,9 @@
+---
+description: Support instructions
+globs: "src/support/**/*.ts"
+alwaysApply: false
+---
+
+# Support
+
+Ask for an order ID before discussing an order.