Echinoids were collected at depth of 0-5 m from coastal water of Larak Island, the Persian Gulf in January 2016. Soft tissues of the animal including peristome, peritoneum, gills, podium, ampulla, axial organ, gonads and food canal were taken and fixed in %10 formalin. Five micron sections were stained by hematoxylin and eosin method and studied under light microscope. The anatomy and histology of organs including peristome, peritoneum, gills, podium, ampulla, axial organ, gonads and food canal were investigated. In oral view, peristome, mouth, teeth, gills, spines, and pedicellariae were the six major compartments. Aboral view was seen as a round shape consisted of tube feet, spines, pedicellariae, madreporite, genital plate, ocular plate and anus. In both oral and aboral view seven types of spines and five types of pedicellariae were reported. Histological evaluation showed the organization of their layers and cells. In this study some anatomical and histological features of the Persian Gulf Echinometra mathaei were characterized. The data presented in this paper could be illuminating the path for marine biologists, anatomists, and histologists to use this creature in their desired research areas, basic or industrial approaches.