The present study aims to apply a high-resolution and label-free proteomics approach to identify and quantify proteins in the eye of zebrafish. First, the results of the present study will provide a comprehensive list of proteins in the eye of zebrafish, and second, establish a platform based on sex-biased proteins that may offer clues to answer crucial questions such as sex-based differences in visual perception and impairments. Our results may improve the outcome of behavioural, developmental, toxicological, and medical experiments considering the zebrafish eye.