Twenty maize inbreds were analyzed using biochemical molecular markers to gain insight into the genetic diversity among three groups viz., low, intermediate and high lysine and tryptophan containing QPM and normal maize lines. Native and denaturing polyacrylamide gel electrophoresis (PAGE) of total soluble seed proteins and three isozyme systems was carried out to examine the storage and functional components, respectively. SDS-PAGE of seed proteins showed variation into the three groups of maize inbred lines. Banding pattern and dendrogram results could clearly differentiate between QPM and normal inbreds along with sub clusters for low and intermediate lysine and tryptophan containing inbred lines. Zymogram patterns of esterase, peroxidase and polyphenol oxidase (PPO) revealed most complex and polymorphic profile for esterase and more diverse for peroxidase isozymes, while PPO being considered as a good biochemical marker and could be used for selecting QPM lines among the normal inbreds. From the current findings, protein electrophoresis could be utilizeeffectively to differentiate QPM and normal maize inbred lines based on variation in banding pattern. Whereas, among the 3 isozyme system, PPO isozyme proved to be useful as protein marker for identification of QPM and normal inbred.