The aim of this study was to research the population structure and genetic diversity of the Nova Scotia Duck Tolling Retriever (NS) and the Lancashire Heeler (LH) dog breeds. Data consisted of nearly all the worldwide registration history for both breeds, including 28,668 NS and 4,782 LH individuals. A reference population, including the females born between 1999 and 2008, was defined for genetic analyses for each breed. Average depth of the pedigrees known for the reference population dogs was 12.9 complete generation equivalents in the NS and 6.0 in the LH. Only a small fraction of the born dogs were used later for breeding. Effective number of founders was 9.8 in the NS and 15.2 in the LH. More than 50% of the genetic diversity in the reference population was explained by two ancestors in the NS and five in the LH. Average inbreeding coefficients in the reference populations were 0.26 in the NS and 0.10 in the LH. Average kinships were 0.26 and 0.08 and realised effective population sizes 18 and 28, respectively. Failure to use available genetic resources for sustainable breeding has resulted in depletion of genetic variation in both breeds. To increase genetic variation, a larger proportion of the dogs should be used in reproduction and the contributions of reproducing animals should be equalized. In the LH, it is necessary to use the unregistered farm dogs in breeding. In the NS, crosses with another breed are needed.