We conducted a 1-year survey of the surface waters of two deep peri-alpine lakes, and investigated the abundances and community structure of picocyanobacteria and co-occurring cyanomyophages. Picocyanobacterial abundances ranged between 4.5x10(4) and 1.6x10(5)cellsmL(-1) in Lake Annecy vs. 2.2x10(3) and 1.6x10(5)cellsmL(-1) in Lake Bourget. Cyanomyoviruses ranged between 2.8x10(3) and 3.7x10(5)copies of g20mL(-1) in Lake Annecy vs. between 9.4x10(3) and 9.4x10(5)copies of g20mL(-1) in Lake Bourget. The structures of picocyanobacteria and cyanomyoviruses differed in the two lakes, and a more pronounced dynamic pattern with greater seasonality was observed in Lake Bourget. At the annual scale, there was no relationship between cyanomyovirus and picocyanobacterial abundances or structures, but we could observe that abundances of the two communities covaried in spring in Lake Bourget. We showed that (i) the changes of picocyanobacteria and cyanomyoviruses were caused by the combined effect of several environmental and biological factors the importance of which differed over time and between the lakes, and (ii) the viral control of the picocyanobacterial community was probably relatively weak at the scale of the investigation.