Protein ubiquitylation plays a major role in the regulation of cellular processes mainly through proteasome-dependent degradation, although it has become increasingly clear that it is also involved in other processes. In the fungus Mucor circinelloides, blue light regulates carotene biosynthesis, with this response controlled by crgA and mcwc-1c genes. CrgA shows characteristics of ubiquitin ligases and represses carotenogenesis in the dark, whereas mcwc-1c is a white collar 1-like gene required for its light induction. Another two white collar 1-like genes have been identified in M. circinelloides: mcwc-1a, which is involved in phototropism, and mcwc-1b, of unknown function. Analysis of double knockout mutants generated for crgA and every mcwc-1 gene demonstrated that crgA and mcwc-1c regulate carotenogenesis by independent pathways. It was also shown that the effect of crgA on carotenogenesis is mediated by mcwc-1b, which acts as a carotenogenesis activator. CrgA is involved in proteolysis-independent mono- and di-ubiquitylation of MCWC-1b, which results in its inactivation. Regulation of carotenogenesis in M. circinelloides by proteolysis-independent ubiquitylation suggests that this mechanism of control could be more widespread than previously thought.