Colletotrichum coccodes (Wallr.) S. Hughes is an important causal agent of potato black dot, but variation among isolates collected in Russia remains insufficiently characterized. In this study, 68 isolates obtained from potato tubers and stems collected in major potato-producing regions of Russia and Belarus were characterized using morphological, physiological, pathogenic, multilocus, and whole-genome approaches. The collection showed variation in colony pigmentation and sclerotial distribution, together with statistically significant differences in colony growth rate and lesion diameter in a wounded detached tuber-slice assay. Among the six isolates tested for temperature response, mean growth was highest at 25 °C among the tested temperatures and was strongly reduced at 35 °C. Multilocus sequence analysis of ITS, act, cal, and his3 loci identified five haplotypes, revealing limited sequence variation in the four loci analyzed and no obvious geographic pattern in this dataset. Comparative genome analysis of two C. coccodes isolates and one C. nigrum isolate revealed high genomic similarity between C. coccodes genomes, conserved repertoires of secreted proteins, effectors, carbohydrate-active enzymes, cytochrome P450 proteins, and secondary metabolite biosynthetic gene clusters, together with 407 orthogroups present in both sequenced C. coccodes isolates and absent from the single C. nigrum genome examined. These findings provide a comprehensive characterization of the collection of C. coccodes isolates from Russia and show that substantial phenotypic variation within the collection was accompanied by limited sequence variation in the analyzed loci, while representatives of two multilocus haplotypes remained highly similar at the whole-genome level.