We determined the complete genomic sequences of two previously discovered insect-specific flaviviruses, Marisma mosquito virus (MMV) and Nanay virus (NANV), using a combination of high-throughput sequencing, reverse transcription-polymerase chain reaction, 5' and 3' rapid amplification of cDNA ends and Sanger sequencing. Complete polyprotein amino acid sequence alignments revealed that the closest known relatives of MMV and NANV are Donggang virus (89% identity, 95% similarity) and Nounané virus (53% identity, 70% similarity), respectively. Phylogenetic inference is in agreement with these findings. Potential programmed -1 ribosomal frameshifting sites were bioinformatically identified in the genomes of both viruses.