Herein, data on rainbow trout infections with the copepod Caligus lacustris in cage aquaculture on Lake Ladoga is presented. Caligus lacustris (n = 127 ex.) were collected from a farm in Lake Ladoga housing cage-reared rainbow trout to describe the size–age and sex structure of the copepod population. Morphological features of the copepods were evaluated according to 10 characters with terminology proposed by Kabata and Gusev (J Linn Soc (Zool) 46(309):155–207, 1966). To determine the phylogenetic position of C. lacustris within the genus Caligus, fragments of the cytochrome c oxidase subunit 1 mitochondrial gene (COI, 645 bp) and 18S rRNA gene (1617 bp) were sequenced. An increase of parasite prevalence was observed as the lake was warming up from July to September. The morphological features of the crustacean’s larval and adult stages, characterized by specific parameters of quantitative traits, are described. Three COI haplotypes and only one 18S rRNA haplotype of C. lacustris were identified among five samples. Based on 18S rRNA analysis (resolution of the COI tree was poor), we can conclude that the clade containing C. lacustris, and the aforementioned sister species, appears as an early radiation of the genus Caligus. The development of freshwater aquaculture contributes to the transfer of the native parasite C. lacustris to farmed rainbow trout.