Indian avian infectious bronchitis virus (IBV) vaccine strains isolated from live attenuated commercial IBV vaccine was characterised based on M and E gene sequence. RNA was extracted and RT-PCR technique was performed to amplify the M and E gene sequence encoding membrane and envelope protein of IBV. Recombinant plasmid named pTZ57R/T-M and pTZ57R/T-E was constructed via inserting the M and E gene into the TA cloning vector, pTZ57R/T respectively. The sequenced M and E gene and its deduced amino acid sequences were compared with the published sequences of reference strains. The M and E gene is of 678 bp and 330 bp in length encoding 225 amino acids and 109 amino acids with a predicted molecular weight of 25.5 kDa and 12.46 kDa respectively. The sequences of the M and E gene share 96.8-99.7% and 82.1-100% homologous identities at nucleotide level with published reference vaccine strain and field isolate strains from different regions and countries respectively. E gene showed significant variation in sequence identities. Phylogenetic tree based on these M and E sequences was generated, and the tree topology suggests that Indian IBV vaccine strain share common ancestor with routinely used reference vaccine strain sequences.