Nine new putative Baeyer-Villiger monooxygenase encoding genes were identified in the eukaryote Yarrowia lipolytica and eight were subsequently cloned and expressed. These enzymes, Yarrowia monooxygenases A-H (YMOA-H), were used in biocatalysis reactions with ketones, sulfides and sulfoxides as substrates. YMOB converts ketones and sulfides, albeit with low activities. However, YMOA did not convert any of the tested ketone substrates, but showed activity towards sulfides and sulfoxides and also showed very high stereoselectivity. This enzyme produced high amounts of sulfones and even converted dimethylsulfoxide (DMSO). Therefore, the sulfoxidation activity of YMOA was investigated in a mutational study. Variants with increased and reduced sulfone yields were created, indicating relevant amino acid positions for the control of sulfoxidation activity. This work expands the set of eukaryotic BVMOs and explores the Yarrowia monooxygenase A, which might belong to a new class of BVMOs as indicated by its unique activity and a phylogenetic analysis.