This protocol describes the transformation of the picoprasinophyte alga Micromonas commoda, a green alga that is found in tropical to temperate oceans. The strain used was genome-sequenced in (1). The original strain name was NOUM17, housed as RCC299. The latter was rendered axenic, genome-sequenced, and deposited at the CCMP (now NCMA) as CCMP2709 and also maintained in the Worden lab. The below protocol is an adaptation of transformation methods used for the choanoflagellate Salpingoeca rosetta. We are grateful to N. King and D. Booth for their invaluable support in initial stages of experiments, as well as help from C. Poirier, M. Hamilton, K. Hoadley, C. Eckmann and especially C. Yung throughout the entire development.