Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important source of bioactive natural products. The cross-links between aromatic amino acid side chains (cyclophane cross-links) confer structural diversity and complexity. These cross-links are primarily catalyzed by two major types of enzymes: radical S-adenosylmethionine (rSAM) enzymes and cytochrome P450 enzymes. This review focuses on the diverse cyclophane cross-linking patterns introduced by rSAM and P450 enzymes during RiPP biosynthesis, and summarizes the similarities and differences between these enzymatic transformations, aiming to provide some insights for the discovery, engineering, and mechanistic study of this class of natural products.