There have been no major advances in understanding the evolution of th
e Old World fruit bats (Megachiroptera: Pteropodidae) since the work o
f Andersen (1912, Catalogue of the Chiroptera in the collection of the
British Museum, 2nd edition, Volume 1, Megachiroptera, British Museum
of Natural History, London), nor have there been any rigorous cladist
ic analyses of megachiropteran interrelationships. Here we report a ph
ylogenetic investigation of restriction endonuclease site variation in
the ribosomal RNA cistrons of 25 species in 14 genera of Indo-West Pa
cific Megachiroptera. Twenty-three of the 82 mapped sites were phyloge
netically informative. Analyses of these informative sites suggest thr
ee considerable modifications to the morphological understanding of me
gadhiropteran relationships: (1) the most-parsimonious explanation of
site-state distribution is that the Macroglossinae (as previously defi
ned) is paraphyletic with respect to other groups; (2) the cynopterine
and rousettine sections are not shown as monophyletic sister groups i
n any of the most-parsimonious trees; and (3) Pteropus and Acerodon ar
e not closely related to any other rousettine genera.