The circular mitochondrial genome of Malawimonas jakobiformis is 47,328 bp in size and codes for 81 genes (some of which are duplicated; see below). Coding regions are tightly packed and protein genes are often separated by three tRNA genes. No introns were detected. A 9.1-kbp-long region, containing genes for the large and small subunit rRNAs (rnl, rns), cox2, nad4L, two ORFs and genes for 11 tRNAs, is repeated in inverted orientation, with the two copies situated approximately opposite one another on the map. Genes are transcribed from both DNA strands.
Protein-coding genes specified by M. jakobiformis mtDNA consist of cob, cox1,2,3, nad1,2,3,4,4L,5,6,9 and atp1,6,8,9, as well as a large set of ribosomal protein genes typical of protist and distinct from animal or fungal mtDNAs. The latter genes include rpl2,5,6,11,14,16,18,19,20,31 and rps1,2,3,4,7,8,11,12,13,14,19. Among these ribosomal protein genes are three that have not been found to date in non-jakobid protist mtDNAs, namely rpl18,19,31. Compared to what is seen in the mitochondrial genomes of the jakobids Reclinomonas americana and Jakoba libera, the order of ribosomal protein genes in M. jakobiformis mtDNA is less reminiscent of the bacterial gene organization in the adjacent str, S10, spc and alpha operons. However, the gene linkage rps13-rps11-rps4 in M. jakobiformis mtDNA is typical of bacteria, whereas in all other mtDNAs, rps4 has either been moved elsewhere in the genome or migrated to the nucleus. Unless rps4 has secondarily been translocated back into the alpha gene cluster of Malawimonas mtDNA, which is quite unlikely, this feature would represent a unique ancestral character and might suggest that Malawimonas, as well as of the entire clade of organisms with discoidal cristae mitochondria, are the most early diverging of mitochondria-containing eukaryotes.
Seven ORFs appear in the mtDNA, two of which (ymf16,39) are also present in other organisms and five of which are unique.
Finally, Malawimonas mtDNA codes for 25 distinct tRNA genes, sufficient to recognize all codons present in protein-coding sequences. The standard genetic code is used in translation.