The species has been found in dry, spiny, and gallery forest, as well as more open habitats, in southwestern Madagascar.

During the 2000s, molecular studies have revealed that the widely distributed African, Eurasian, and Australian genus Miniopterus is much more species-rich than previously thought.

[1] In 2008 and 2009, however, Steven Goodman and colleagues presented evidence that the former concept of M. manavi in fact encompassed five morphologically and molecularly distinct species of small Miniopterus.

[3] The five recognized species of M. manavi-like bats are not each other's closest relatives, but apparently acquired their similarities through convergent evolution.

[4] Analysis of sequences of the mitochondrial cytochrome b gene suggested that M. brachytragos is most closely related to another Malagasy species, M. sororculus.

[6] Although samples of M. mahafaliensis differed from each other by a maximum of 2.2% in their cytochrome b, Goodman and colleagues could not discern any phylogeographic structure within the species.

[4] Little is known of the ecology of M. mahafaliensis, but species of Miniopterus generally feed on insects, breed seasonally, and roost in large colonies in caves.