The plant used in the characterization of Fragaria chiloensis latent virus (FClLV) contained double-stranded RNA (dsRNA) bands that did not correspond in size to the genomic or subgenomic RNAs of known strawberry viruses. Using shotgun cloning, sequences of a cryptic virus, named Fragaria chiloensis cryptic virus (FCCV), were obtained. This communication presents the complete genome sequence of FCCV. The genome of FCCV consists of three monocistronic RNAs, an unusual feature for cryptic viruses that are normally bipartite. The largest molecule encodes an RNA-dependent RNA polymerase, while the other two encode closely related proteins predicted to be the coat proteins of the virus. Phylogenetic analysis showed that FCCV is related most closely to members of the fungi-infecting Partitivirus genus rather than members of the plant-infecting Alphacryptovirus, providing a possible insight into the evolution of cryptic viruses. More than 300 strawberry plants from North and South America were tested for FCCV, and the virus was only detected in plants from South America.