This study investigated a resident community of Atlantic spotted dolphins (Stenella frontalis) on Little Bahama Bank (LBB) in the Bahamas utilizing a noninvasive molecular approach. Genetic template material was collected and extracted from fecal material of S. frontalis. Fine-scale population structure was found within LBB according to mitochondrial DNA (mtDNA) and microsatellites (Fst = 0.25317, P < 0.0001 and Fst = 0.04491, P < 0.0001, respectively). Three main social clusters (North, Central, South/Roam) exist on LBB and all clusters were found to be genetically distinct according to microsatellite analyses. Mitochondrial haplotypes revealed North and South/Roam were not differentiated, but Central was different from both. When separated by sex, males were less genetically structured than females. Males showed no evidence of structure according to Ost or Rst.