Currently the biosynthesis of rhodoquinone (RQ) is still being debated, but there are two main biosynthetic pathways that are being researched. The first pathway requires the organism to produce ubiquinone (UQ) before the amino group can be added onto the quinone ring. The second pathway allows RQ to be synthesized without any UQ being present by using tryptophan metabolites instead.
In the case of the prokaryotic organism R. rubrum, RQ has been shown to be synthesized by addition of an amino group to a pre-existing UQ; thus UQ needs to be present as a precursor before RQ can be made. Figure 1 shows the biosynthesis of UQ in yeast and E. coli where ‘n’ represents the number of isoprene units between various organisms. Dimethylallyl diphosphate A and isopentyl diphosphate B come together to form polyisoprenyl diphosphate C. With the addition of p-hydroxybenzoic acid, the product that arises is 3-polyprenyl-4-hydroxybenzoic acid D. The next three steps of synthesis varies between different organisms, but molecule E is made across all organisms and through oxidation, demethyldemethoxyubiquinone (DDMQ) is eventually formed.  RQ has been theorized to be synthesized from DDMQn, DMQn, DMeQn, or UQn, as shown with the dashed arrows. Recent studies have shown that Path 4 - RQ biosynthesis via UQ, is the favored route.  It has been further shown that the gene rquA is required for the biosynthesis of RQ in R. rubrum, and that RquA catalyzes the conversion of UQ to RQ. The RquA protein uses S-adenosyl-L-methionine as the amino donor to convert UQ to RQ in an unusual Mn(II)-catalyzed reaction.
Research in C. elegans has shown an alternative path for production of RQ. Even after knocking out all UQ production, RQ is still present within those mutant strains. Based on this data, RQ production is not solely based on UQ-like molecules and instead can be made via tryptophan metabolites. Therefore, the amino group that is added in late stages of RQ biosynthesis in rquA-containing species is instead present throughout intermediate stages of RQ biosynthesis in C. elegans. With this proposed biosynthesis, the kynurenine pathway still needs to be upregulated, and activity from certain genes like kynu-1 which encodes for the KYNU-1 enzyme that catalyzes production of 3-hydroxy-L-kynurenine to 3-hydroxyanthranilic acid, needs to be upheld.  Recent work has revealed that alternative splicing of the coq-2 polyprenyltransferase gene controls the level of RQ in animals.  Animals that produce RQ (e.g. C. elegans and helminth parasites) contain both COQ-2 protein isoforms (COQ-2a and COQ-2e), and COQ-2e catalyzes prenylation of 3-hydroxyanthranilic acid (instead of p-hydroxybenzoic acid) which leads to RQ.