Sea urchins are ecologically important marine invertebrates with recognized medical, nutritional, and ecological significance. This study aimed to investigate the morphological characteristics of the sea urchin Echinometra mathaei collected from the Northern Red Sea, Gulf of Suez, Egypt, in September 2022. Simultaneously, the anticancer activity of a petroleum ether extract derived from the exoskeleton of E. mathaei was evaluated against the human liver cancer cell line HepG2. The results showed significant variation in weight, with the largest specimen weighing 80.4 g and the smallest 18.6 g. Diameter ranged from 3 to 7 cm and height varied from 1.5 to 3.5 cm. The maximum test length and total length were 6 and 9.5 cm, respectively, with minimum values of 2.5 and 5 cm. The length-weight relationship (LWR), diameter-weight relationship (DWR), and height-weight relationship (HWR) indicated a negative allometric growth trend (b ≠ 3, p > 0.001). The extract exhibited cytotoxic activity against HepG2 cells, with IC50 values of 65.58 µg/ml at 24 hours and 23.21 µg/ml at 48 hours. Using flow cytometry analysis, the extract caused significant enrichment of G1 and S phases in HepG2 cells, confirming cell cycle arrest and apoptosis induction. These findings demonstrate that the petroleum ether extract from the exoskeleton of E. mathaei induces apoptosis in HepG2 cells, confirming its cytotoxic effect. Therefore, it emphasizes the potential of this marine-derived extract as a source of novel anticancer therapeutics.