Purpose: This protocol describes how to negatively or positively stain viruses that have been deposited onto TEM grids so that they can be imaged using transmission electron microscopy (TEM). Positive staining stains the virus itself such that the virus is dark against a lighter background (Figure 1A). This is the easiest staining to do and yields results suitable for analyzing the morphological diversity of viruses from aquatic samples. Negative staining relies on some stain remaining around the edges of a virus such that the details of the virus are clearly defined (Figure 1B). Negative staining is more difficult and is used to obtain publication quality micrographs of viruses.Note: To deposit viruses onto the grids prior to staining, use either the \u201cAdsorbing Viruses onto TEM Grids\u201d protocol or the \u201cQuantitatively Depositing Viruses onto TEM Grids\u201d protocol. Grids should be stained immediately after depositing viruses onto them.