Aim: Mucor indicus is a zygomycetes fungus with several advantages. Its ethanol yield from hexoses rivals that of Saccharomyces cerevisiae and it is capable of producing ethanol from xylose in limited aerobic conditions. It is also able to ferment dilute acid hydrolysate and is known to be dimorphic; able to grow in both filamentous and yeast-like modes. Methods: In this study, the difference between yeast-like and filamentous cells of M. indicus was investigated using modern polymerase chain reaction (PCR) techniques. Four mRNA sequences were detected with a higher expression in the filamentous growth form than in the yeast-like, by a factor of 1.3-4.2. One of the sequences was novel and three have been detected in another species of Mucor, M. circinelloides, coding for a chitin synthase, a proteasome and a sigma 70 factor. Results and conclusion: The novel sequence exhibited the largest difference in expression and was subjected to knock-down. However, it proved to be best suited for detection of emerging growth patterns, since the knock-down had little effect on the developing growth form. With the results of this study, an important step towards understanding the difference in the dimorphic behaviour exhibited by M. indicus, as well as other members of the genus Mucor, has been taken. Potentially it could also be used as one of the tools for the control of the dimorphic behaviour of M. indicus, and other species of the Mucor genus.