The sequence diversity of the entire mitochondrial control region (CR) of three meadow viper (Vipera ursinii) populations was analysed and compared to previously documented nuclear genetic variability at the major histocompatibility complex (MHC) Class I loci. One of the populations, a small and inbred Hungarian population, exhibited no MHC polymorphism, whereas the two other, sampled from large viper populations in Ukraine, shoved very high MHC diversity. In spite of the great difference in population size and nuclear (MHC) diversity, all of the vipers from the three populations exhibited a CR haplotype diversity of zero. The dramatic discrepancy in nuclear vs. mitochondrial variability in the Ukrainian viper populations suggest that the lack of CR diversity was not caused by a population bottleneck, but rather by slow CR evolutionary rate, which has been documented in numerous other vertebrate taxa. Thus, due to the large taxonomic differences in CR rate of evolution, population genetic diversity estimates based on CR heterogeneity (and conservation management decisions that spring from those estimates) may depend as much upon the taxa being investigated, as upon the underlying pattern of genetic variation within the study population.