ABSTRACT Considerable research has shown that cyanobacteria and the viruses that infect them (cyanophage) are pervasive and diverse in global lake populations. Few studies have seasonally analyzed freshwater systems, and little is known about the bacterial and viral communities that coexist during the harsh winters of the Laurentian Great Lakes. Here, we employed quantitative PCR to estimate the abundance of cyanomyoviruses in this system, using the portal vertex g20 gene as a proxy for cyanophage abundance and to determine the potential ecological relevance of these viruses. Cyanomyoviruses were abundant in both the summer and the winter observations, with up to 3.1 × 10 ⁶ copies of g20 genes ml ⁻¹ found at several stations and depths in both seasons, representing up to 4.6% of the total virus community. Lake Erie was productive during both our observations, with high chlorophyll a concentrations in the summer (up to 10.3 μg liter ⁻¹ ) and winter (up to 5.2 μg liter ⁻¹ ). Both bacterial and viral abundances were significantly higher during the summer than during the winter ( P < 0.05). Summer bacterial abundances ranged from 3.3 × 10 ⁶ to 1.6 × 10 ⁷ ml ⁻¹ while winter abundances ranged between ∼3.4 × 10 ⁵ and 1.2 × 10 ⁶ ml ⁻¹ . Total virus abundances were high during both months, with summer abundances significantly higher at most stations, ranging from 6.5 × 10 ⁷ to 8.8 × 10 ⁷ ml ⁻¹ , and with winter abundances ranging from 3.4 × 10 ⁷ to 6.6 × 10 ⁷ ml ⁻¹ . This work confirms that putative cyanomyoviruses are ubiquitous in both summer and winter months in this large freshwater lake system and that they are an abundant component of the virioplankton group.