Infectious bronchitis virus (IBV) is one of the major poultry pathogens of global importance.  However, the prevalent of IBV strains in Malaysia are poorly characterized. The partial genomic sequences (6.8 Kb) comprising the S-3a/3b-E-M-Intergenic region-5a/5b-N gene order of 11 Malaysian IBVs isolated in 2014 and 2015 were sequenced using next-generation sequencing technology. Phylogenetic and pairwise sequence comparison (PASC) analysis showed that the isolated IBVs are divided into 2 groups. Group 1 (IBS124/2015, IBS125/2015, IBS126/2015, IBS130/2015, IBS131/2015 IBS138/2015 and IBS142/2015) shared 90% - 95% nucleotide and deduced amino acid similarities to QX-like. Among these isolates, IBS142/2015 is the first IBV detected in Sarawak state located at East Malaysia (Borneo Island). Meanwhile, IBV isolates in Group 2 (IBS037A/2015, IBS037B/2015, IBS051/2015 and IBS180/2015) were 91.62% and 89.09% identical to Malaysian variant strain MH5365/95 (EU086600) at nucleotide and amino acid levels respectively. In addition, all studied IBVs were distinctly separated with Massachusetts (70 – 72% amino acid similarity), European strains including 793/B, Italy-02 and D274 (68 – 73% amino acid similarity). Viruses in Group 1 have the insertion of 3 amino acids at positions 23, 121 and 122 of S1 protein and recombinant events detected at nucleotide position 4354-5864 with major parental sequence derived from QX-like (CK-CH-IBYZ-2011) and a minor parental sequence derived from Massachusetts vaccine strain (H120). This study demonstrated the coexistence of IBV Malaysian variant strain a long with the QX-like strain in Malaysia