Highlights • The morphology of the abalone Haliotis squamata and Haliotis diversicolor squamata are very similar. • The results of genetic identification in Haliotis squamata and Haliotis diversicolor squamata species using COI genes from mitochondria show an average difference in genetic distance of 16%. • From the results of this study, we propose that the abalone from the southern waters of Java and Bali be separated species, H. squamata Reeve 1846.