The circular mitochondrial genome of Cafeteria roenbergensis is 43.2 kbp in size and contains no introns. C. roenbergensis mtDNA encodes those protein genes most commonly found in other mitochondrial genomes, including nad1,2,3,4,4L,5,6, cob, cox1,2,3, and atp6,8(= orfB),9. The genome also encodes two rRNA genes (rns, rnl) and genes for 20 tRNAs, which are sufficient to recognize all but 3 codons in protein-coding sequences.
In addition, C. roenbergensis mtDNA specifies a number of protein genes that are not found in the more derived animal or fungal mtDNAs, but instead are rather typical of protist mtDNAs. These include nad7,9,11, atp1, rpl2,6,14,16, and rps2,4,8,12,13,14,19). Four unique, long ORFs have also been found (orf1006, orf781, orf294, orf443).
The tightly packed genes in C. roenbergensis mtDNA are separated by A+T-rich intergenic regions and are transcribed from the same DNA strand, the sole exception being nad5.
The mitochondrial translation code in C. roenbergensis is not the standard genetic code, in contrast to what is seen in its closest known relatives, Phytophthora infestans and Ochromonas danica; instead, UGA is preferentially translated as tryptophan.