This study presents a detailed anatomical and histological investigation of the sea urchin Echinometra mathaei, emphasizing unique morphological structures and site-specific variations. In March 2023, echinoids were collected from two sites in the northern Red Sea at depths ranging from 0 to 5 meters. Various soft tissues, including the peritoneum, peristome, gills, podium, ampulla, and food canal, were extracted and preserved in 10% formalin. Sections of five microns were prepared and stained using the haematoxylin and eosin technique, followed by examination under a light microscope. The study concentrated on the external anatomy revealed distinct oral and aboral structures, including spines, pedicellariae, tube feet, and gills, with measurements indicating notable size and weight differences between specimens from the two collection sites. Internally, the digestive, nervous, and water vascular systems, as well as Aristotle's lantern and gonads, were described in detail. Histological analysis highlighted cellular arrangements in key structures such as the peristome, esophagus, stomach, and intestines, with unique features identified in connective tissues and epithelial layers. A key finding of this study is the observation of tricephalous pedicellariae, expanding the taxonomic understanding of E. mathaei. Morphological variations in tube feet ossicles between collection sites suggest environmental or genetic influences. Additionally, the ultrastructure of spines and stereom provided new insights into their composition and function. This comprehensive analysis enhances the knowledge of E. mathaei's anatomy, contributes to echinoid systematics, and underscores its ecological adaptations across varying habitats.