Danio rerio is a widely utilized model organism, particularly in molecular evolution and developmental studies. However, the sex determination of this species remains an area of interest. The focus has been on chromosome 4, that contains a sex-linked region and has similar properties to known sex chromosomes (Anderson et al. 2012). Nevertheless, it has been observed that some of the domesticated zebrafish strains lack this sex associated region (Wilson et al. 2014). Additionally, we observe a wide structural variation between domesticated and wild strains within this specific chromosome. Our study applies comparative genomics to identify structural variation between different Danio rerio strains, as well as compared to closely related species, primarily with the focus on the chromosome 4. This includes the analysis of transposable elements that compose half of the genome of zebrafish and stand largely behind the structural variation (Howe et al. 2013). To look at the variation in this highly repetitive genome we utilize long read Oxford Nanopore sequencing technology. Our study will help to understand the variation within this model organism, on the nuclear as well as mitochondrial level, and bring more light to the movement of transposable elements.