The living Malagasy prosimians and their recently extinct subfossil relatives include about 20 genera and 8 families that can be considered one contemporenous fauna. They exhibit morphological, behavioral, and ecological differences comparable to living anthropoid primates. This diversity is matched by the equally varied topography, climate, and vegetation of Madagascar. To investigate habitat-related size variation, skull lengths of wild-caught adults were used to compare sizes of closely-related conspecific and congeneric “sister taxa.” More than 1,550 museum specimens were examined representing virtually all known forms of extant and subfossil Malagasy prosimians. A total of 98 pairwise, sister-taxa comparisons among 76 different taxa from six broadly defined ecogeographic regions revealed a consistent pattern of size variation: (1) the smallest Malagasy prosimians inhabit the semiarid forests, bush, and thickets of the South; (2) next largest are those from the dry deciduous forests of the West and the humid but seasonal forests of the Sambirano; (3) larger yet are those from humid tropical and secondary forests of the East; and (4) the largest of all are the extinct forms of the central highlands that lived in what was probably a savanna-bush-woodland mosaic in the past but is now grasslands devoid of living prosimians. Taxa from the extreme North are more variable in size (small, intermediate, or large), which may reflect the mixture of local habitats in northern Madagascar. The ecogeographic size differences may be adaptive responses related to the carrying capacity of local environments such that smaller-sized species are favoured where the resources they exploit are more limited. Field observations on behavioral thermoregulation, home range size, and population densities offer some support for this hypothesis. Ecologically induced size differences among local populations were probably one factor in speciation events leading to the modern diversity of the Malagasy primates.