Whilst the use of molecular genetic techniques is widespread in the fields
of population and evolutionary biology, their application within the mammal
ian order Chiroptera neither reflects the species richness nor the ecologic
al and behavioural diversity of the order. This is despite the fact that th
e Chiroptera are problematic to study using more direct observational techn
iques. Here, we standardize and synthesise the current data, assess the con
tribution of molecular research to the study of bat species and highlight t
he importance of its continued and expanded use. At an inter-population lev
el, molecular studies have demonstrated a great diversity of population gen
etic structure within the order. Among populations of migratory species, ge
netic structure appears universally low, and hence seasonal movement is lik
ely to be the prevailing influence. However, for sedentary species an array
of factors including dispersal ability, extrinsic barriers to gene flow an
d historical events may determine the extent of genetic partitioning among
populations. Intrinsic factors such as wing morphology or roost requirement
s may also influence population genetic structure in sedentary bat species,
a proposal which requires further research. Molecular studies have also ma
de important contributions towards an understanding of social organisation
in bats. Evidence indicates that in many polygynous species male mating suc
cess does not translate directly into reproductive success, perhaps as a re
sult of multiple mating by females. Estimates of relatedness within and gen
etic structure among colonies are, in general, very low; a finding which ha
s important implications regarding theories concerning the formation and pe
rsistence of bat social groups. Molecular studies have provided new and imp
ortant insights into the ecology of bats, and have opened up exciting and p
reviously unexplored avenues of research. The data from these studies sugge
st not only a predictive framework for future studies, but also the use of
genetic data in the management and conservation of bat species.