Based on second generation sequencing (MiSeq platform, Illumina), we determined the genetic diversity of T4-like bacteriophages of the family Myoviridae by analysing fragments of the major capsid protein gene g23 in the plankton of Lake Baikal. The sampling depth in our study was significantly higher than in those obtained by the Sanger method before. We obtained 33 701 sequences of the g23 gene fragments, 141 operational taxonomic units (OTUs) of which were identified. 86 OTUs (60.9%) had the closest relatives from lakes Bourget and Annecy, and 28 OTUs (19.8%) had the highest identity with the Baikal g23 clones, which had been previously identified in the northern and southern basins of the lake by the Sanger method. The remaining OTUs were similar to the clones from other ecosystems. We showed a high genetic diversity of T4-type bacteriophages and a genetic difference with the phage communities from other ecosystems.