We describe a highly polymorphic microsatellite panel for identifying individual leopards using DNA from scat. After successfully screening 16 published microsatellites, we optimized a panel of 7 microsatellites that yields a Probability of Identity between siblings value of 5.24E−04. We used this panel to identify 217 individuals from 287 leopard scats collected from five tiger-reserves in Central India. We identified 101 males and 92 females by amplifying a fragment of the Amelogenin protein gene. This panel will be helpful to study genetic structure, gene flow, relatedness and sex ratio of leopards.