Coronaviruses (CoVs) are characterized by high recombination frequencies, resulting in sudden outbreak of newly evolved viruses with different pathogenicity, tissue tropism and high genome sequence variability. Recently, an outbreak of CoVs was evolved in the Arabian Pennsylvania, which is known as Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Full genome sequence analysis of MERS-CoV isolates and its comparison with other CoV full genome sequences revealed a low to medium sequence identity. Furthermore, it showed more sequence identity and phylogenetic relations with bat-derived CoVs and lower values with animal-derived CoVs, indicating low possibility of zoonotic origin and possible incrimination of bats in the spread of MERS-CoV. The higher neighbor homology was evident with BetaCoV and their associated SARS-CoV. The spike protein, which is a highly variable part of CoV genome and responsible for difference in tissue tropism and virus entry to the cell, showed more or less similar profile of the whole genome analysis. Furthermore, the highest identity was with those in bats with Asian origin of CoV and there was lower homology with isolates from other continents. With low human-to-human transmission and low homology with CoV of animal origin, bats are thought to be the source of MERS-CoV, especially those bearing the Asian isolates of CoV.