Sea urchins are valuable marine creatures that live in the waters of Indonesia, and typically found in seagrass and coral reefs. This study aimed to determine the distribution of sea urchins and the benthic characteristics that serve as their habitat using high resolution drone images. Object-based image analysis (OBIA) with a support vector machine algorithm is used to identify benthic habitats, while the distribution of sea urchins is determined by thresholding pixel values. A total of 812 aerial photos with a spatial resolution of 3.98 cm/px were obtained and mapped into five classes of benthic habitat (sand, rubble, seagrass, living coral, and dead coral algae). The dominant habitat class obtained was dead coral algae, with an area of 234,035 m2 (29.63%), whereas seagrass was the smallest, with an area of 74,149 m2 (9.39%). The overall accuracy of the benthic classes was 65.44%, with kappa coefficient value of 0.57. The study found that the total number of sea urchins on Lancang Island was 61,551. The dominant distribution of sea urchins was found in the living coral class with 18,094 individuals, but the highest density was in the rubble class with 1358 individuals/ha.