‘Egusi’ melon Citrullus lanatus (Thunb.) Matsum. & Nakai is an important vegetable crop in Nigeria, grown for its edible seeds and oils. The diverse areas in which the crop is cultivated make it a rich source of genetic resources for the species. To explore its diversity, 50 accessions of ‘egusi’ melon were collected from different agro-ecological parts of Nigeria and were evaluated using 25 simple sequence repeat (SSR) markers. A total of 49 bands were scored, of which 42 were polymorphic, accounting for 93.60% of the polymorphic loci. The PIC value ranged from 0.36–0.80. UPGMA cluster analysis revealed five distinct groups for SSR. PCA analysis revealed the distinction of the accessions NG/OE/MAR/09/014, NG/TO/APR/09/027 and A8. Based on the results of this study, SSR markers appear to be particularly useful for the estimation of genetic similarity among diverse accessions of melon.