Eastern Canis latrans (Coyote) dispersed into northeastern North America during the last century and into Nova Scotia in the 1970s. En route, Coyotes hybridized extensively with C. lycaon (Eastern Wolf). Coyote populations in northeastern North America contain mitochondrial and nuclear DNA characteristics of both species. In samples collected from Nova Scotia, Prince Edward Island, New Brunswick, and Newfoundland, we found mitochondrial DNA haplotypes characteristic of Coyote and/or Eastern Wolf with decreasing haplotype diversity consistent with sequential founder events/bottlenecks moving from west to east generally and on islands. Principal components analysis of a suite of morphological characters indicated that male eastern Coyotes from Nova Scotia with Eastern Wolf mitochondrial DNA are significantly larger than male eastern Coyotes from the same region with Coyote mitochondrial DNA.