diff --git a/internal/manifest/validate.go b/internal/manifest/validate.go
index 727c6ba..c09bd34 100644
--- a/internal/manifest/validate.go
+++ b/internal/manifest/validate.go
@@ -1,6 +1,8 @@
 package manifest
 
 import (
+	"bytes"
+	"encoding/json"
 	"fmt"
 	"sort"
 	"strings"
@@ -41,9 +43,131 @@ func Validate(data []byte) ([]ValidationError, error) {
 		}
 	}
 
+	// Check for duplicate flag keys
+	duplicates := findDuplicateFlagKeys(data)
+	for _, key := range duplicates {
+		issues = append(issues, ValidationError{
+			Type:    "duplicate_key",
+			Path:    fmt.Sprintf("flags.%s", key),
+			Message: fmt.Sprintf("flag '%s' is defined multiple times in the manifest", key),
+		})
+	}
+
 	return issues, nil
 }
 
+// findDuplicateFlagKeys parses the raw JSON to detect duplicate keys within the "flags" object.
+// Standard JSON unmarshaling silently accepts duplicates (taking the last value), so we use
+// a token-based approach to detect them.
+func findDuplicateFlagKeys(data []byte) []string {
+	decoder := json.NewDecoder(bytes.NewReader(data))
+
+	// Navigate to the root object
+	token, err := decoder.Token()
+	if err != nil || token != json.Delim('{') {
+		return nil
+	}
+
+	// Look for the "flags" key at the top level
+	for decoder.More() {
+		keyToken, err := decoder.Token()
+		if err != nil {
+			return nil
+		}
+
+		key, ok := keyToken.(string)
+		if !ok {
+			continue
+		}
+
+		if key == "flags" {
+			return findDuplicatesInObject(decoder)
+		}
+
+		// Skip the value for non-"flags" keys
+		skipValue(decoder)
+	}
+
+	return nil
+}
+
+// findDuplicatesInObject reads an object from the decoder and returns any duplicate keys.
+func findDuplicatesInObject(decoder *json.Decoder) []string {
+	token, err := decoder.Token()
+	if err != nil || token != json.Delim('{') {
+		return nil
+	}
+
+	seen := make(map[string]bool)
+	var duplicates []string
+
+	for decoder.More() {
+		keyToken, err := decoder.Token()
+		if err != nil {
+			break
+		}
+
+		key, ok := keyToken.(string)
+		if !ok {
+			continue
+		}
+
+		if seen[key] {
+			duplicates = append(duplicates, key)
+		} else {
+			seen[key] = true
+		}
+
+		// Skip the value
+		skipValue(decoder)
+	}
+
+	// Consume the closing brace
+	_, err = decoder.Token()
+	if err != nil {
+		return duplicates
+	}
+
+	// Sort for consistent output
+	sort.Strings(duplicates)
+
+	return duplicates
+}
+
+// skipValue advances the decoder past one complete JSON value (object, array, or primitive).
+func skipValue(decoder *json.Decoder) {
+	token, err := decoder.Token()
+	if err != nil {
+		return
+	}
+
+	switch t := token.(type) {
+	case json.Delim:
+		switch t {
+		case '{':
+			// Skip object contents
+			for decoder.More() {
+				if _, err := decoder.Token(); err != nil { // key
+					return
+				}
+				skipValue(decoder)
+			}
+			if _, err := decoder.Token(); err != nil { // closing }
+				return
+			}
+		case '[':
+			// Skip array contents
+			for decoder.More() {
+				skipValue(decoder)
+			}
+			if _, err := decoder.Token(); err != nil { // closing ]
+				return
+			}
+		}
+	}
+	// Primitives (string, number, bool, null) are already consumed by the Token() call
+}
+
 func FormatValidationError(issues []ValidationError) string {
 	var sb strings.Builder
 	sb.WriteString("flag manifest validation failed:\n\n")
diff --git a/internal/manifest/validate_test.go b/internal/manifest/validate_test.go
index eaafd4b..5413be8 100644
--- a/internal/manifest/validate_test.go
+++ b/internal/manifest/validate_test.go
@@ -5,6 +5,189 @@ import (
 	"testing"
 )
 
+func TestValidate_DuplicateFlagKeys(t *testing.T) {
+	tests := []struct {
+		name           string
+		manifest       string
+		wantDuplicates []string
+	}{
+		{
+			name: "no duplicates",
+			manifest: `{
+				"flags": {
+					"flag-a": {"flagType": "boolean", "defaultValue": true},
+					"flag-b": {"flagType": "string", "defaultValue": "hello"}
+				}
+			}`,
+			wantDuplicates: nil,
+		},
+		{
+			name: "single duplicate",
+			manifest: `{
+				"flags": {
+					"my-flag": {"flagType": "boolean", "defaultValue": true},
+					"my-flag": {"flagType": "string", "defaultValue": "hello"}
+				}
+			}`,
+			wantDuplicates: []string{"my-flag"},
+		},
+		{
+			name: "multiple duplicates",
+			manifest: `{
+				"flags": {
+					"flag-a": {"flagType": "boolean", "defaultValue": true},
+					"flag-b": {"flagType": "string", "defaultValue": "hello"},
+					"flag-a": {"flagType": "integer", "defaultValue": 42},
+					"flag-b": {"flagType": "float", "defaultValue": 3.14}
+				}
+			}`,
+			wantDuplicates: []string{"flag-a", "flag-b"},
+		},
+		{
+			name: "triple duplicate of same key",
+			manifest: `{
+				"flags": {
+					"repeated": {"flagType": "boolean", "defaultValue": true},
+					"repeated": {"flagType": "string", "defaultValue": "hello"},
+					"repeated": {"flagType": "integer", "defaultValue": 42}
+				}
+			}`,
+			wantDuplicates: []string{"repeated", "repeated"},
+		},
+		{
+			name: "empty flags object",
+			manifest: `{
+				"flags": {}
+			}`,
+			wantDuplicates: nil,
+		},
+		{
+			name: "manifest with schema field",
+			manifest: `{
+				"$schema": "https://example.com/schema.json",
+				"flags": {
+					"dup": {"flagType": "boolean", "defaultValue": true},
+					"dup": {"flagType": "boolean", "defaultValue": false}
+				}
+			}`,
+			wantDuplicates: []string{"dup"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			issues, err := Validate([]byte(tt.manifest))
+			if err != nil {
+				t.Fatalf("Validate() error = %v", err)
+			}
+
+			var gotDuplicates []string
+			for _, issue := range issues {
+				if issue.Type == "duplicate_key" {
+					// Extract the flag key from the path (format: "flags.key")
+					parts := strings.SplitN(issue.Path, ".", 2)
+					if len(parts) == 2 {
+						gotDuplicates = append(gotDuplicates, parts[1])
+					}
+				}
+			}
+
+			if len(gotDuplicates) != len(tt.wantDuplicates) {
+				t.Errorf("got %d duplicates, want %d", len(gotDuplicates), len(tt.wantDuplicates))
+				t.Errorf("got duplicates: %v", gotDuplicates)
+				t.Errorf("want duplicates: %v", tt.wantDuplicates)
+				return
+			}
+
+			for i, want := range tt.wantDuplicates {
+				if gotDuplicates[i] != want {
+					t.Errorf("duplicate[%d] = %q, want %q", i, gotDuplicates[i], want)
+				}
+			}
+		})
+	}
+}
+
+func TestValidate_DuplicateKeyErrorMessage(t *testing.T) {
+	manifest := `{
+		"flags": {
+			"my-flag": {"flagType": "boolean", "defaultValue": true},
+			"my-flag": {"flagType": "string", "defaultValue": "hello"}
+		}
+	}`
+
+	issues, err := Validate([]byte(manifest))
+	if err != nil {
+		t.Fatalf("Validate() error = %v", err)
+	}
+
+	var found bool
+	for _, issue := range issues {
+		if issue.Type == "duplicate_key" {
+			found = true
+			if issue.Path != "flags.my-flag" {
+				t.Errorf("expected path 'flags.my-flag', got %q", issue.Path)
+			}
+			expectedMsg := "flag 'my-flag' is defined multiple times in the manifest"
+			if issue.Message != expectedMsg {
+				t.Errorf("expected message %q, got %q", expectedMsg, issue.Message)
+			}
+		}
+	}
+
+	if !found {
+		t.Error("expected to find a duplicate_key validation error")
+	}
+}
+
+func TestFindDuplicateFlagKeys_EdgeCases(t *testing.T) {
+	tests := []struct {
+		name     string
+		input    string
+		expected []string
+	}{
+		{
+			name:     "invalid JSON",
+			input:    "not valid json",
+			expected: nil,
+		},
+		{
+			name:     "array instead of object",
+			input:    `["a", "b", "c"]`,
+			expected: nil,
+		},
+		{
+			name:     "no flags key",
+			input:    `{"other": "value"}`,
+			expected: nil,
+		},
+		{
+			name:     "flags is not an object",
+			input:    `{"flags": "string value"}`,
+			expected: nil,
+		},
+		{
+			name:     "flags is an array",
+			input:    `{"flags": [1, 2, 3]}`,
+			expected: nil,
+		},
+		{
+			name:     "nested duplicates not detected in flag values",
+			input:    `{"flags": {"flag1": {"nested": 1, "nested": 2}}}`,
+			expected: nil,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := findDuplicateFlagKeys([]byte(tt.input))
+			if len(result) != len(tt.expected) {
+				t.Errorf("got %v, want %v", result, tt.expected)
+			}
+		})
+	}
+}
+
 // Sample test for FormatValidationError
 func TestFormatValidationError_SortsByPath(t *testing.T) {
 	issues := []ValidationError{