Isoalloxazine is the structural foundation of flavins such as riboflavin (vitamin B2) and is a heterocyclic compound. It has a tricyclic structure which means it has three interconnected rings of atoms and is a tautomer of alloxazine. The structure is formed by primary-secondary aromatic o-diamines and they are a high-melting crystalline substance. The R-group is used to attach various flavin groups It has a similar structure to pteridines which has two interconnected rings. Isoalloxazine was first obtained in 1934 by Richard Kuhn an Austrian-German biochemist and lab mates.

Isoalloxazine rings can exist in different redox and ionization states depending on the chemistry of FMN and FAD associated with it. Using the redox-active isoalloxazine system, FAD and FMN are able to do one and two electron transfer reactions and also be coupled with proton transfers.