The partial genomic sequences (6.8 kb) analysis of the S-3a/3b-E-M-intergenic region-5a/5b-N gene order of 11 Malaysian IBVs isolated in 2014 and 2015 indicated that the IBV strains can be classified into 2 groups as Malaysian QX-like and variant strains. Group I (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 the QX-like strain. Meanwhile, IBV isolates in Group II (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. Viruses in Group I have the amino acids mutations of the S1 protein and recombinant resembling QX viruses. The pathogenicity of IBS130/2015 (QX-like) and IBS037A/2014 (variant) in 1-day-old and 30-day-old specific-pathogen-free (SPF) chickens were further characterized.  Even though both strains caused respiratory and kidney infections based on immunohistochemistry (IHC), real-time quantitative PCR (qPCR) and ciliostasis study, the results showed that QX-like strain was more pathogenic, caused higher mortality and showed higher tissue tropism to the kidney than the variant strain. On the other hand, the Malaysian variant strain although causing low or no mortality depending on the age of the infected chickens, the virus showed high tissue tropism to the respiratory tracts than the QX-like strain. This study demonstrated coexistence of pathogenic IBV Malaysian variant strain along with the QX-like strain in Malaysia.