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Simple Summary: Bimodal karyotypes, including both large chromosomes and microchromosomes, are mainly found in reptiles, birds, fish, and insects, but not mammals. Studies of microchromosomes are currently of great interest. The karyotype of the snake Vipera berus is a prime example of a bimodal karyotype. We conducted a comparative cytogenetic study of meiotic (synaptonemal complexes in prophase I) and mitotic chromosomes. A significant asynchrony in the assembly of meiotic bivalents and the dynamics of the appearance of the mismatch repair protein MLH1 were analyzed, and a high level of meiotic recombination was shown. Furthermore, minor species-specific markers of the V. berus meiotic karyotype were identified. Vipera berus is the species with the largest range of snakes on Earth and one of the largest among reptiles in general. It is also the only snake species found in the Arctic Circle. Vipera berus is the most involved species of the genus Vipera in the process of interspecific hybridization in nature. The taxonomy of the genus Vipera is based on molecular markers and morphology and requires clarification using SC-karyotyping. This work is a detailed comparative study of the somatic and meiotic karyotypes of V. berus, with special attention to DNA and protein markers associated with synaptonemal complexes. The karyotype of V. berus is a remarkable example of a bimodal karyotype containing both 16 large macrochromosomes and 20 microchromosomes. We traced the stages of the asynchronous assembly of both types of bivalents. The number of crossing-over sites per pachytene nucleus, the localization of the nucleolar organizer, and the unique heterochromatin block on the autosomal bivalent 6—an important marker—were determined. Our results show that the average number of crossing-over sites per pachytene nucleus is 49.5, and the number of MLH1 sites per bivalent 1 reached 11, which is comparable to several species of agamas. [ABSTRACT FROM AUTHOR]