Genetic diversity in livestock populations is a significant contributor to the sustainability of animal production, and also, it allows animal production to become more responsive to environmental changes and market demands. The loss of genetic diversity poses a potential plateau in production and may also result in loss of fitness or viability in animal production. In this study, we investigated the rate of inbreeding (ΔF) and effective population size (Ne) as important quantitative indicators of genetic diversity and evaluated the effect of the recent implementation of genomic selection on the loss of genetic diversity in North American Holstein and Jersey. Pedigree and genotype data of 214,566 and 95,732 Holstein and Jersey animals, respectively, born between 1990 and 2018 inclusively were provided by the Canadian Dairy Network (CDN). Estimated average pedigree inbreeding coefficient was 7.74 and 7.20% for Holsteins and Jerseys, respectively. The corresponding values for the genomic inbreeding coefficient was 13.61 for Holsteins and 21.16% for Jerseys. Generation interval for the whole 29-year time period averaged approximately 5 years for all selection pathways combined. The ΔF per generation was estimated to be 1.03, 1.64% for Holstein animals and 0.54 and 0.42% for Jersey animals using pedigree and genotype data, respectively. The estimated effective population size ranged from 30 to 48 animals for Holsteins and 93 to 119 animals for Jerseys. The current state of genetic diversity following the implementation of genomic selection calls for measures and means of controlling the rate of inbreeding, which will help to manage and maintain farm animal genetic resources.