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This species of mongoose is sympatric with Herpestes edwardsii in much of its native range and can be readily distinguished from the latter species by its much smaller size. The body is slender and the head is elongated with a pointed snout. The length of the head and body is 509–671 millimetres (20.0–26.4 in). The ears are short. They have five toed feet with long claws. Genders differ in size with males having a wider head and bigger bodies. They use about 12 different vocalizations
Currently, there isn’t a study that has determined the preferred habitat for the Javan mongoose in its native range, however observations of trap success of the animal provides some insight . In studies where traps were used in an attempt to remove the mongoose, it was found that the trap success was nearly zero in conditions of rain. This information, along with other reports of the Javan mongoose’s strong dislike for rain, suggests that the mongoose prefers very dry habitats. There are studies that note the preferred habitats of the Javan mongooses introduced to other places such as Thailand, the Caribbean islands, Hawai’i, and Nepal. However, these preferences vary and do not provide information regarding the mongoose in its natural habitat.