The colour hue and saturation of the fish skin are important factors in fish breeding, reflecting the momentary physiological status of the fish. Algorithms evaluating fish colour were created in the MATLAB environment and compiled in the stand-alone application, Expertomica Fishgui. Fish groups fed on several diets (varying in carotenoid supplements) were compared as concerns image analysis methods on colour changes. Images were processed and evaluated to locate body positions, areas and colour saturation. Conversion from the Red-Green-Blue (RGB) colour space to chromatic colours was carried out to reduce the colour space. The threshold of skin chromatic colour was set on basis of the chromatic histograms using Otsu automatic bimodal segmentation. The average colour was calculated through all pixels of the selected area in the original image and through all images of the group. Colour conversion to the Hue-Saturation-Value (HSV) colour space was also carried out. Relative deviation between the saturation of samples in the control and the experimental groups provided a means of judgement. The dominant wavelength was also determined.