Little is known about the effect of El Niño Southern Oscillation-induced fires on the genetic diversity of tropical rainforest species. Here, I report on the isolation and characterization of 10 microsatellite loci, five loci each, for two lycaenid butterfly species in East Kalimantan, Indonesia, namely Drupadia theda and Arhopala epimuta , which will be used to specifically study the impact of disturbance on genetic diversity. Microsatellite enrichment was carried out using streptavidin-coated magnetic beads. Positive colonies were identified with the three-primer polymerase chain reaction (PIMA). Cross-species amplifications conducted both within and between genera were successful in 16 out of 20 tests.