Epifluorescent microscopy was used to determine the abundance of viruses in samples from marine and freshwater environments and in laboratory cultures that were filtered onto 0.02-μm pore-size filters and stained with a cyanine-based dye (Yo-Pro-1). High counting efficiency, ease of preparation, modest equipment requirements, and the possibility of preparing specimens for long-term storage, make the Yo-Pro-based method ideal for routine environmental analysis.