The collector urchin, Tripneustes gratilla is an ecologically crucial sea urchin community with typical habitats consisting of shallow seagrass beds or reefs. Samples were obtained from the Red Island Beach, Banyuwangi Regency, East Java, Indonesia. Nucleotide sequencing analysis was conducted on mitochondrial cytochrome oxidase subunit I (coi) DNA fragments amplified by PCR. Nucleotide sequences ranging from 605 to 606 base pairs were collected from 16 specimens at the sample site. Through DNA barcoding analysis, it was determined that all samples are of the Tripneustes gratilla species. Phylogenetic studies were conducted by comparing the gene sequences of the collecting urchin haplotypes identified in this study with gene sequences of identical base pair length from GenBank and T. ventricosus, which served as the reference group. The phylogenetic trees exhibited good consistency and clearly delineated distinct clades for each species. Phylogenetic status of haplotype and the existence of sea urchins were documented. The clarification of the evolutionary position of ecologically important species offers fundamental information for potential future conservation efforts of such species.