The Snow Mountain agent (SMA) is the prototype genogroup II and serotype 3 human calicivirus responsible for epidemic outbreaks of acute gastroenteritis. We have cloned the region of the SMA genome that encodes the single capsid protein. The predicted amino acid sequence of the capsid protein is distinct from other calicivirus strains that have been termed SMA-like based on sequence similarity between the RNA polymerase regions and IEM reactivity. In a previous report, a high sequence similarity in a small region of the RNA polymerase between SMA and another strain, OTH-25, suggested that the capsid proteins of OTH-25 and SMA would be very similar. In this report, we show that the capsid proteins of OTH-25 and SMA are more distinct than was predicted by similarity in the RNA polymerase. In addition, phylogenetic analysis of a region of the RNA polymerase and of the N-terminal conserved domain of the capsid protein of 12 human caliciviruses resulted in trees with different topologies, suggesting that recombination has occurred within this group of viruses. Molecular characterization of the prototype calicivirus strains is important in determining the relationships between capsid similarity at the amino acid level, genetic grouping by sequence comparison, and antigenic reactivity.