While studying packs of the eastern timber wolf in Algonquin Provincial Park in Ontario, DNA profiles at 8 microsatellite loci and the mitochondrial control region were found to be similar to those of the red wolf, C. rufus. Based on this it was suggested that both the red wolf and the eastern timber wolf have a common origin, evolving in North America, with the coyote diverging from them 150,000-300,000 years ago and with neither having any recent connection with the gray wolf that evolved in Eurasia. It was further proposed, that the eastern timber wolf retain its original species designation of C. lycaon instead of the present status of a subspecies of the gray wolf. Four "types" or "races" of wolves have been previously described in Ontario. Using DNA profiles, assignment tests identified four groups, which were typified by animals in Algonquin Provincial Park, Pukaskwa National Park, Frontenac Axis and those north of Lake Superior. The tests indicate that Frontenac animals are hybrids between the western coyote and C. lycaon and represent the eastern coyote. Pukaskwa maintains a small wolf population, which is genetically closer to the gray wolves of the Northwest Territories than the surrounding C. lycaon. These may represent an isolated remnant population of the original "Ontario type" (C. lupus). Animals north of Lake Superior were identified as C. lycaon, but represent products of hybridization between C. lycaon and C. lupus. Currently within Ontario, Algonquin Park contains the largest protected area of the eastern timber wolf. DNA profiles, including Y-linked microsatellite loci were used to establish maternity, paternity and kin relationships for 102 animals from 24 packs over a 12-year period. A complex pack structure was identified. A pack is not composed simply of an unrelated breeding pair and their offspring and subordinates appear to enter pack systems through adoption, pack splitting, dispersal and immigration. Relatively high genetic structuring was found between the Park animals and the "Tweed" wolves to the southeast suggesting introgression of coyote genetic material is not a present concern to the integrity of park animals. Evidence of gene flow with animals to the west, northeast and northwest coupled with the high genetic diversity, suggest that the Park animals are not an island population, but the southern part of a larger metapopulation of C. lycaon. Increased interest in the relationship of the red and eastern wolves led to the investigation of a gene in the major histocompatibility complex. Allelic variation in the exon 2 region of the DLA-DQA1 locus was analysed for gray wolves, red wolves, the eastern timber wolf and the western coyote. Twelve alleles were identified, seven of which were previously characterized in dogs. Non-synonomous nucleotide substitutions was 3.0 times higher than the synonomous changes, indicative of strong positive selection. These data provide baselines for the determination of allele frequencies and their distribution across the geographical range of the four species in North America. The results in this thesis have sparked numerous debates with respect to the protection of the wolves in Algonquin Provincial Park and reintroduction of wolves into Northeastern United States. The data support the idea that the C. lycaon population in Ontario is relatively large, numbering in the thousands rather than the hundreds. Concern for the conservation of wolves in Ontario should be directed at the declining numbers of gray wolves present in Ontario. / Thesis / Master of Science (MSc)