The Javan and small Indian mongooses, ranging from the Middle East to South‐east Asia, are considered as two species or as a single species, varying in size and colour from west to east. In order to clarify their systematic status and to define the limits of their ranges, Cytochrome b sequences were obtained from 27 specimens, and localities of 392 specimens from museum collections were determined. The phylogenetic analyses revealed that the Javan and Small Indian mongooses grouped in two separate clades with their range limits located in Myanmar. The Javan mongoose is in fact closer to the grey mongoose than to the small Indian mongoose.