Haemosporidians infect a wide diversity of bat genera and species, yet little is known about their transmission cycles or epidemiology. Though several recent studies have focused on the genus
Hepatocystis
, an Old World parasite primarily infecting bats, monkeys, and squirrels, this group is still understudied with little known about its transmission and molecular ecology. These parasites lack an asexual erythrocytic stage, making them unique from the
Plasmodium
vertebrate life cycle. In this study, we detected a prevalence of 31% of
Hepatocystis
in short-nosed fruit bats (
Cynopterus brachyotis
) in Singapore. Phylogenetic reconstruction with a partial
cytochrome b
sequence revealed a monophyletic group of
Hepatocystis
from
C. brachyotis
in Malaysia, Singapore, and Thailand. There was no relationship with infection and bat age, sex, location, body condition or monsoon season. The absence of this parasite in the five other bat species sampled in Singapore indicates this
Hepatocystis
species may be host restricted.