Allpahuayo virus was initially isolated from arboreal rice rats (Oecomys bicolor and Oecomys paricola) collected during 1997 at the Allpahuayo Biological Station in northeastern Peru. Serological and genetic studies identified the virus as a new member of the Tacaribe complex of the genus Arenavirus. The small (S) segment of the Allpahuayo virus prototype strain CLHP-2098 (Accession No. AY012686) was sequenced, as well as that of sympatric isolate CLHP-2472 (Accession No. AY012687), from the same rodent species. The S segment was 3382 bases in length and phylogenetic analysis indicated that Allpahuayo is a sister virus to Pichinde in clade A. Two embisense, nonoverlapping reading frames were identified, which result in two predicted gene products, a glycoprotein precursor (GPC) and a nucleocapsid protein (NP). A predicted stable single hairpin secondary structure was identified in the intergenic region between GPC and NP. Details of the genetic organization of Allpahuayo virus are discussed.