Two flying squirrel species,Pteromys momongaandPteromys volanscontain 2nequals;38 with the same fundamental number of 68, but differ in their karyotypes. Almost all the autosomes and the sex chromosomes have either complete or partial G-band correspondence, and thus provide definitive evidence for the taxonomic relationship of thesePteromysspecies. The karyotypic differences occurred as results of pericentric inversion, tandem fusion, and deletion of autosomes and the Y chromosome. No Robertsonian event occurred. Both species possess one pair ofAg-NORs in identical G-banded chromosomes but different morphology resulting from pericentric inversion. Despite the conservatism of G-band patterns, a striking accumulation of C- heterochromatin has occurred in theP. momongakaryotype. Flow-cytometric DNA determination demonstrated that P.volansgenome contains approximately 15 %% less DNA. These differences seem to be prima rily reflected by chromosomal deletions in the P.volanskaryotype rather than ac cumulation of the Cheterochromatin in the P.momongakaryotype. The present findings are crucial for explaining the direction of karyotype evolution of these species, and suggest that the karyotype of P.momongais ancestral and that P.volansis derived from it.