The large family of cytochrome P450 enzymes are heme containing proteins generally associated with the cytoplasmic face of the endoplasmic reticulum in Eukaryotic cells. They play essential roles in detoxification mechanisms of cellular processes and are key components in biosynthesis and evolution of specialized metabolites having various biological activities in the plant kingdom. The assembly of complex monoterpenoid indole alkaloids and benzylisoquinoline alkaloids involves numerous cytochrome P450 enzymes that participate in their chemical diversification and that act as central scaffolds for recruitment of the biosynthetic enzymes required for their production. The present review discusses the roles played by different CYP families (-71, -72, -75, -76, 80-, 82-, -86 and -719) in the diversification of MIA and BIA pathways that have been discovered and characterized. Recent studies using homology model guided site-directed mutagenesis coupled with determination of biochemical function are described that provide insights about how small modifications in protein structures allowed the evolution of new substrate specificity and the appearance of new monoterpenoid indole alkaloids and benzylisoquinoline alkaloids in Nature.