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The interpretation of a signal sent by the mtDNA cytb gene as a molecular marker in phylogenetic and population genetic research can be complicated by cumulative influence of parallel mutations, i.e., the entropy of nucleotide sequences. Such a phenomenon impedes differentiation among the effects of hybridization, natural polymorphisms, and artifacts imposed by pseudogenes. We analyzed possible limitations in the use of the mtDNA cytb gene as a molecular marker by the example of the Apodemus genus. For this purpose, the entropy of nucleotide sequences was calculated, and probable tracts of gene conversion were sought in samples of various Apodemus species from Tibet, Korea, south of Russian Primorye, and Western Europe. Many haplotypes were identified as containing tracts of gene conversion. The high level of nucleotide sequence variability was found in species from Tibet, particularly, in A. draco, presumably due to the influence of low effective sizes of populations on the speed of point mutation accumulation and also cytochrome b role in the adaptation to unfavorable environment. The effects of hypervariability in cytb nucleotide sequences of some samplings resulting in entropy growth imitating gene conversion when compared to other species of the genus were analyzed. Examples of possible pseudogene interference among published cytb sequences are provided. It is suggested that the strategy in the use of the mtDNA cytb gene in population genetics and phylogenetics should be adapted to the degree of the gene variability. Emphasis is placed on the necessity of close control over sequencing data.