diff --git a/src/mutahunter/core/controller.py b/src/mutahunter/core/controller.py
index 393c2c1..9e1fa00 100644
--- a/src/mutahunter/core/controller.py
+++ b/src/mutahunter/core/controller.py
@@ -11,11 +11,14 @@
 from mutahunter.core.db import MutationDatabase
 from mutahunter.core.entities.config import MutationTestControllerConfig
 from mutahunter.core.error_parser import extract_error_message
-from mutahunter.core.exceptions import (CoverageAnalysisError,
-                                        MutantKilledError, MutantSurvivedError,
-                                        MutationTestingError,
-                                        ReportGenerationError,
-                                        UnexpectedTestResultError)
+from mutahunter.core.exceptions import (
+    CoverageAnalysisError,
+    MutantKilledError,
+    MutantSurvivedError,
+    MutationTestingError,
+    ReportGenerationError,
+    UnexpectedTestResultError,
+)
 from mutahunter.core.git_handler import GitHandler
 from mutahunter.core.io import FileOperationHandler
 from mutahunter.core.llm_mutation_engine import LLMMutationEngine
@@ -93,7 +96,9 @@ def run_mutation_testing_all(self) -> None:
         all_covered_files = self.coverage_processor.file_lines_executed.keys()
         for covered_file_path in tqdm(all_covered_files):
             if FileOperationHandler.should_skip_file(
-                covered_file_path, self.config.exclude_files
+                covered_file_path,
+                exclude_files=self.config.exclude_files,
+                only_mutate_file_paths=self.config.only_mutate_file_paths,
             ):
                 continue
             executed_lines = self.coverage_processor.file_lines_executed[
@@ -114,7 +119,9 @@ def run_mutation_testing_diff(self) -> None:
         )
         for file_path in tqdm(modified_files):
             if FileOperationHandler.should_skip_file(
-                file_path, self.config.exclude_files
+                file_path,
+                exclude_files=self.config.exclude_files,
+                only_mutate_file_paths=self.config.only_mutate_file_paths,
             ):
                 continue
             modified_lines = GitHandler.get_modified_lines(file_path)
diff --git a/src/mutahunter/core/io.py b/src/mutahunter/core/io.py
index e89f90d..73ae16a 100644
--- a/src/mutahunter/core/io.py
+++ b/src/mutahunter/core/io.py
@@ -47,14 +47,16 @@ def prepare_mutant_file(
         return mutant_path
 
     @staticmethod
-    def should_skip_file(filename: str, exclude_files: List[str]) -> bool:
-        for file_path in exclude_files:
-            if not os.path.exists(file_path):
-                raise FileNotFoundError(f"File {file_path} does not exist.")
-            return all(file_path != filename for file_path in exclude_files)
+    def should_skip_file(
+        filename: str, exclude_files: List[str], only_mutate_file_paths: List[str]
+    ) -> bool:
+        if only_mutate_file_paths:
+            for file_path in only_mutate_file_paths:
+                if not os.path.exists(file_path):
+                    raise FileNotFoundError(f"File {file_path} does not exist.")
+            return all(file_path != filename for file_path in only_mutate_file_paths)
         if filename in exclude_files:
             return True
-        return any(keyword in filename for keyword in TEST_FILE_PATTERNS)
 
     @staticmethod
     def check_syntax(source_file_path: str, source_code: str) -> bool: