Several workers have suggested that multilocus multilocus variable number of tandem repeat (VNTR) based ‘DNA fingerprints’ are not useful in detecting differentiation among outbred populations. They suggest that the extremely high mutation rates and complexity associated with multilocus VNTR fragments make detection of interpopulation differences against a background of extremely high intrapopulation variation unlikely. This paper shows that DNA fingerprinting with the multilocus VNTR probes (GACA)4 and (CT)9 reveal significant population differences in VNTR frequencies between Florida and Georgia populations of the outbred, abundant and vagile fish species Poecilia latipinna. Differences in mutation rates among some VNTR loci may account for the ability to detect interpopulation differentiation with these probes. These results suggest that appropriate species/probe combinations would allow investigations of population structure on a microgeographical scale even in outbred species with multilocus VNTR probes where less-sensitive techniques have failed.