In all the plant kingdom there is a single order, Caryophyllales, that contains taxa that have replaced anthocyanins with a chemically distinct yet functionally identical pigment, betalains. Betalains are tyrosine derived red and yellow pigments produced through a proposed three enzymatic step pathway. Thus far only one of these three genes and no regulators have been reported. Transcriptome analysis of red Beta vulgaris and other betalain producing Caryophyllales species using Next-Generation sequencing facilitated the discovery of several betalain genes including identification of two 75 year old classical beet pigment loci, R and Y. A highly expressed Cytochrome P450 (CYP76AD1) was determined through silencing, overexpression and genetic studies to be one of the unknown biosynthetic steps. It corresponds to the classical locus R, and required for producing red betalains. It was hypothesized that the betalain pathway may have co-opted the anthocyanin regulators because both pigment types are produced in the same temporal and spatial pattern. Analysis of transcriptome data revealed a MYB type transcription factor homologous to the MYBs that regulate anthocyanin pigments. Silencing and overexpression studies have shown that the identified MYB regulates the production of betalains through regulation of the two biosynthetic pathway enzymes, CYP76AD1 and DODA. Genetic analysis of the MYB has mapped it to the locus Y approximately 7.5 cM from CYP76AD1/R verifying the classical mapping data. Use of modern genomic techniques has allowed the identification of two long sought loci while allowing the creation of the first genetic network in a nutritionally and evolutionarily interesting pathway.