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¹ Universitas Gadjah Mada, Faculty of Agriculture, Department of Fisheries Jl. Flora 1A Bulaksumur, Depok, Sleman, Yogyakarta 55281 DOI : 10.4194/GA893 Viewed : 77 - Downloaded : 48 The diversity of sea urchins in Indonesia significantly differs throughout various aquatic environments. Sea urchins serve as a keystone species and as an indicator of coastal ecosystem health. Colobocentrotus atratus, commonly referred to as the helmet urchin, is a distinctive sea urchin endemic to the south coast of Java, originating from Hawaii. This research aims to identify the species, determine the genetic distance, and analyze the phylogenetic relationship of the C. atratus sea urchin that lives on the south coast of Java. Sampling occurred at Ngrumput Beach, Yogyakarta, Indonesia. Nucleotide sequence analysis was conducted on the COI mitochondrial DNA amplified using PCR. Nucleotide sequences ranging from 625 base pairs were obtained from three specimens of C. atratus. Molecular analysis indicates that these samples were identified as Colobocentrotus atratus. Phylogenetic analysis was performed by comparing the haplotype gene sequences of C. atratus from the south coast of Java with gene sequences of identical base pair length, utilizing Diadema setosum as the outgroup. The phylogenetic study results indicate that C. atratus from the south coast of Java is closely related to C. atratus from Sabang and France. This research provides essential data that can support future initiatives to preserve coastal ecosystems. Keywords : Colobocentrotus atratus Coi Sea urchin Endemic species Diversity