Two species of mongoose reported from Pakistan (Herpestes javanicus and H. edwardsii) are sympatric in many areas of their distribution range in the Potohar Plateau. Morphologically, the two species differ in their body size, so there could be substantial anatomical differences between them, not yet documented. The current study compared morphological and anatomical characteristics of the two species inhabiting the Potohar Plateau. Results showed marked morphological and anatomical differences between two mongoose species studied. External morphometrical characteristics including body weight, length of fore limbs, hind limbs and snout length of the two species differed significantly (p < 0.05). Among anatomical parameters, among females, liver weight and heart length of the two species differed significantly (p < 0.05). Among males, significant differences were found between heart length (p < .001), weight of large intestine, stomach, liver and lungs, and weight of right and left testes (p < 0.05) of the two mongoose species. Other anatomical variables of the two species differed non-significantly (p > 0.05).