The genetic population structure of the precominant zooplankter, the copepod Calanus finmarchicus (Gunnerus), was examined to determine whether genetically distinct populations exist in the Gulf of Maine. C. finmarchicus was sampled in three regions of the Gulf of Maine (Great South Channel, spring 1989; northern Gulf of Maine, winter 1990; Great South Channel and Georges Bank, spring 1990). Copepods from seven locations in the Great South Channel, five in the northern Gulf of Maine and four on or near Georges Bank were assayed for allozyme variation and mitochondrial DNA variation of amplified 16S rRNA and cytochrome b genes. Restriction fragment length polymorphism (RFLP) analyses of both mitochondrial DNA genes revealed no variation among any of the individuals assayed. Analysis of five polymorphic allozyme loci revealed that genetic variation among the three geographic regions was low, and genetic identities were high between all locations (I>0.97). Most of the genetic variation was among locations regardless of region. Chi-square tests were used to examine genetic similarity between specific pairs of locations within and between regions. In the northern Gulf of Maine, genetic homogeneity occurred over larger spatial scales (hundreds of km) than in either the Great South Channel or Georges Bank (tens of km). Only copepods from the Bay of Fundy and Nova Scotian Shelf locations were genetically distinct from Wilkinson Basin copepods at two loci. Copepod populations from the northern locations may have been partially isolated or they may represent immigrant populations (e.g., from the Gulf of St. Lawrence). Several pairs of locations were genetically distinct at one or more loci in the two southern regions. Differences between locations in these regions may represent distinct populations advected into the areas at different times or from different sources (e.g., genetic variation may represent a mixture of genetically distinct northern and southern copepod populations). These results suggest extensive gene flow among populations of C. finmarchicus in the Gulf of Maine with some evidence of genetic population subdivision near the Gulf's northeastern and southern boundaries.