The results of karyological and cytogenetic studies of populations of conifer species from the families Pinaceae and Cupressaceae growing under extreme conditions have been summarized. A chromosomal variability has been revealed in coniferous plants growing at the southern and northern borders of their natural habitats, at ecological limits of distribution, in anthropogenically disturbed ecosystems, and under introduction conditions. A high frequency of changes in the number of chromosomes (mixoploidy, aneuploidy, and polyploidy) and their morphology has been observed. Different types of chromosomal anomalies (ring and polycentric chromosomes, chromosome fragments, and multiple chromosomal abnormalities), chromosome agglutination, mitotic and meiotic abnormalities, and the appearance of B chromosomes have been revealed. Using classical methods and fluorescent in situ hybridization (FISH), a polymorphism of nucleolar-forming regions of chromosomes has been studied and features of the 5S and 45S ribosomal DNA loci have been revealed.