Abstract Bryde’s whales (Balaenoptera brydei) differ
from other typical baleen whale species because they
are restricted to tropical and warm temperate waters in
major oceans, and frequent trans-equatorial movement
has been suggested for the species. We tested this
hypothesis by analyzing genetic variation at 17 microsatellite
loci (N = 508) and 299 bp of mitochondrial
DNA (mtDNA) control region sequences (N = 472) in
individuals obtained from the western North Pacific,
South Pacific, and eastern Indian Ocean. Combined
use of microsatellite and mtDNA markers allowed us
to distinguish between contemporary gene flow and
ancestral polymorphism and to describe sex-specific
philopatry. A high level of genetic diversity was found
within the samples. Both nuclear and mtDNA markers
displayed similar population structure, indicating a lack
of sex-specific philopatry. Spatial structuring was
detected using both frequency-based population
parameters and individual-based Bayesian approaches.
Whales in the samples from different oceanic regions
came from genetically distinct populations with evidence
of limited gene flow. We observed low mtDNA
sequence divergence among populations and a lack of
concordance between geographic and phylogenetic
position of mtDNA haplotypes, suggesting recent
separation of populations rather than frequent transequatorial
and inter-oceanic movement. We conclude
that current gene flow between Bryde’s whale populations
is low and that effective management actions
should treat them as separate entities to ensure continued
existence of the species.