Technical Abstract: To date, no data have been generated on the population genetics of Trichinella due to the lack of genetic markers and the difficulty of working with such small parasites. In the Arctic region of North America and along the Rocky Mountains, there exists two taxonomic genotypes of Trichinella, Trichinella nativa and Trichinella T6, respectively, which are well differentiated by biochemical and molecular characters. However, both are resistant to freezing, show other common biological characters and produce fertile F1 offspring upon interbreeding. A single GTT trinucleotide present in the ITS-2 sequence of T. nativa but not in Trichinella T6 was used as a genetic marker to study gene flow within this character under both experimental and natural conditions. As expected, all F1 larvae showed a heterozygote pattern in the GTT character upon heteroduplex analysis; however, within the F2 population, the number of observed heterozygotes (n = 52) was substantially higher than expected (n = 39.08), as supported by the Fis index, and was not in the Hardy-Weinberg equilibrium. In 2 of the 16 (12.5%) Trichinella positive Alaskan wolves, only the Trichinella T6 pattern and the T. nativa/Trichinella T6 hybrid pattern, was observed. No larva showed the T. nativa pattern suggesting that the two genotypes do not have equal weight in the transmission of their respective genetic arrays. Our data demonstrate that Trichinella nativa and Trichinella T6 live in sympatry at least in Alaskan wolves, where T. nativa appears more frequently (69%) than Trichinella T6 (31%). One explanation for this phenomenon is that the last glacial period may have caused a geographical relocation, colonization and independent evolution of T. nativa within the Rocky Mountains, resulting in a bifurcation of the freeze resistant genotype.