Security is an important issue in biometric recognition systems. In recent years, many researchers proposed to use watermarking to improve the security of biometric systems, but some people concern whether the embedded watermarks will influence recognition results. In this paper, we investigate the effects of several fragile and semi-fragile watermarking methods on the iris recognition performance. Experimental results demonstrate that, even images are fully embedded, fragile watermarking methods nearly have no effects on the recognition performance, while semi-fragile watermarking methods which embed watermark in the visually important components of images have larger effects on the recognition performance than the semi-fragile watermarking methods that embed watermark in the visually unimportant components of images. And embedding parameters, such as embedding strength and watermark length, also have some influences on the recognition results.