Abstract
Sea urchins are invertebrates playing a crucial ecological role in maintaining a balance within intertidal ecosystems and serve as bioindicators, in addition to their significant economic value as marine resources. This study aims to investigate sea urchins at Ngrumput Beach, Yogyakarta through ecological index analysis, abundance measurements, and morphological and molecular identification using the DNA barcoding approach. Sampling was from November to December 2023, using a 1x1 m quadrat transect method. Molecular identification targeted the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene. On the basis of morphological and molecular identification, the identified sea urchin species were Echinometra oblonga, Echinometra mathaei, Heterocentrotus trigonarius, and Stomopneustes variolaris. The results indicated that the sea urchins at Ngrumput Beach had an abundance of 74.14 individuals/m2, a species diversity index of 1.07 (moderate), an evenness index of 0.83 (high), and a dominance index of 0.23 (low). Distribution pattern analysis revealed that Echinometra oblonga and Stomopneustes variolaris exhibited clumped distributions, while Heterocentrotus trigonarius and Echinometra mathaei displayed both uniform and clumped distributions. The highest sea urchin abundance was observed 30 meters from the shoreline. Molecular identification revealed a DNA sequence length of 630 bp. DNA barcoding analysis, including phylogenetic tree construction using the neighbour-joining method and genetic distance evaluation, supported the morphological analysis results.