diff --git a/src/batdetect2/cli/train.py b/src/batdetect2/cli/train.py
index 8d5836a..af2c1b6 100644
--- a/src/batdetect2/cli/train.py
+++ b/src/batdetect2/cli/train.py
@@ -7,6 +7,7 @@ from loguru import logger
 
 from batdetect2.cli.base import cli
 from batdetect2.data import load_dataset_from_config
+from batdetect2.targets import load_target_config
 from batdetect2.train import (
     FullTrainingConfig,
     load_full_training_config,
@@ -20,6 +21,7 @@ __all__ = ["train_command"]
 @click.argument("train_dataset", type=click.Path(exists=True))
 @click.option("--val-dataset", type=click.Path(exists=True))
 @click.option("--model-path", type=click.Path(exists=True))
+@click.option("--targets", type=click.Path(exists=True))
 @click.option("--ckpt-dir", type=click.Path(exists=True))
 @click.option("--log-dir", type=click.Path(exists=True))
 @click.option("--config", type=click.Path(exists=True))
@@ -42,6 +44,7 @@ def train_command(
     ckpt_dir: Optional[Path] = None,
     log_dir: Optional[Path] = None,
     config: Optional[Path] = None,
+    targets: Optional[Path] = None,
     config_field: Optional[str] = None,
     seed: Optional[int] = None,
     train_workers: int = 0,
@@ -62,12 +65,18 @@ def train_command(
     logger.info("Initiating training process...")
 
     logger.info("Loading training configuration...")
+
     conf = (
         load_full_training_config(config, field=config_field)
         if config is not None
         else FullTrainingConfig()
     )
 
+    if targets is not None:
+        logger.info("Loading targets configuration...")
+        targets_config = load_target_config(targets)
+        conf = conf.model_copy(update=dict(targets=targets_config))
+
     logger.info("Loading training dataset...")
     train_annotations = load_dataset_from_config(train_dataset)
     logger.debug(