Univariate and multivariate statistical analyses of skull and external morphology of Aethalops alecto from high mountains in Java (10 specimens), Bali I. (7) and Lombok I. (20) reveal little or no sexual dimorphism. However, measurements of the majority of the 35 skull and 19 external characters differ significantly between these populations.Analyses of skull, and to a lesser extent external characters, indicate that the Javan population is separate in discriminant function space from the Bali and Lombok populations (which are close together). These populations of Aethalops alecto are distinct from Aethalops aequalis from Sabah, Borneo.Protein electrophoresis reveals that populations of Aethalops show levels of genetic variation that are near the mammalian average. Genetic differentiation of populations is low. Thus, despite the fact that Aethalops populations are restricted to high mountains they do not appear to have low effective populations sizes nor are they distinctly genetically isolated.The Bali/Lombok populations are described herein as Aethalops alecto boeadii subsp. nov.