The circular mitochondrial genome of Rhodomonas salina is 48,063 bp in size and codes for 64 genes. Genes are tightly packed, except in a particular region of 4,424 nt that contains long tandem and inverted repeats. Intergenic regions, when present, are A+T-rich. Transcribed genes are found on both DNA strands. The standard genetic code is used for translation.
Among non-jakobid protists, R. salina contains the largest set of mitochondrial genes, including the protein-coding genes nad1,2,3,4,4L,5,6,7,8,9,10,11, cob, cox1,2,3 and atp1,6,8,9. Ribosomal protein genes typical of protist but not animal or fungal mtDNAs include rpl5,6,15,16 and rps3,4,7,8,11,12,13,14,19. Of 7 ORFs encoded by R. salina mtDNA, 2 (ymf16,39) are also present in the mtDNA of other organisms, 3 are intronic ORFs, and 2 are unique. Three succinate dehydrogenase genes (sdh2-4) present in the R. salina mitochondrial genome are rarely found in mtDNA. These genes are clustered as in eubacterial genomes and in Reclinomonas americana mtDNA.
Finally, the mtDNA codes for large subunit (rnl) and small subunit (rns) rRNA genes and 26 tRNA genes. Two group II introns, one having 1 and the other 2 intronic ORFs are localized in the cox1 gene.