The decline of ornamental fish populations in their native habitats due to over-fishing has brought about the development of ornamental fish aquaculture, to which fish of the Anabantoidei suborder are important contributors. The genetic variations among species of this suborder were examined by mitochondrial gene sequencing analysis using the cytochrome b and 12S genes. According to the cytochrome b gene, the most similar strains were Trichogaster trichopterus (gold) and Trichogaster trichopterus (blue) (100%). Trichogaster leerii was less similar to them (86.0%), and an even lower similarity was found between the species T. trichopterus and Trichogaster labiosus (85.6%). The least similarity was observed between Betta betta and the genera Colisa (50.2%) and Trichogaster (60.1%). The phylogenetic trees of 12S and cytochrome b were very similar. According to 12S, the similarity between Trichogaster species was high (91.4% - 100%), and between species of this genus and Colisa lalia, it was lower (88.4%). In conclusion, sequence analyses, based on cytochrome b and 12S can provide a useful tool for the study of the systematic relationships between species belonging to the Anabantoidei suborder. Moreover, it may support other parameters used in systematics. Thus, these genes may be applied as genetic markers in aquaculture.