Abstract: Recent emergence of Chikungunya virus has attracted the researchers to explore its whole genome to predict the structural changes at the genetic level during disease outbreak. Present study was aimed to investigate the mutational patterns at the genome level in Chikungunya virus using advanced software programs. Pair-wise analysis of whole genome (n = 84) of Chikungunya virus revealed that structural genes mutated 2.6 times higher than non-structural genes. The chronological analysis showed that the Chikungunya virus prevalent during 2008 mutated higher than any other outbreaks recorded so far. Number of singleton sites in the variable region of viral genome was found higher when compared to number of parsimonous sites. Chronological and geographical scale analysis of the viral outbreak showed that about 30% of viral genome was subjected to mutation so far. Chikungunya virus isolated from Malaysian geography had underwent more mutations when compared anyother geographical locations. Highest number of singleton mutations were observed in Chikungunya viruses isolated from Malayasian geography whereas highest number of parsimonous informative sites were observed in Chikungunya isolates of India. The mutational analysis also revealed that viral genome contained two times more singleton sites compared to parsimonious sites. About 1207 nucleotides in the structural protein coding region of Chikungunya virus genome was identified as a unique DNA signature witch could be used in precise and fast diagnosing of Chikungunya virus in future.