Java

I have about 5000 images with water marks on them and 5000 identical images with no watermarks. The file names of each set of images are not correlated to each other in any way. I'm looking for an API in Java preferably that I can use to pair each water marked image with its non-water marked pair.

Can Java be used for image processing?

Java provides immediate access to the image pixels and color information and allows conversions and image processing.

Is Python good for image recognition?

Python is one of the widely used programming languages for this purpose. Its amazing libraries and tools help in achieving the task of image processing very efficiently.

You can use the OpenCV library. It can be used in Java. Please follow http://docs.opencv.org/doc/tutorials/introduction/desktop_java/java_dev_intro.html

Regarding image compare, you can see another useful answer here: Checking images for similarity with OpenCV