Nipah virus, member of the Paramyxoviridae family, is classified as a Biosafety Level‐4 agent and category C priority pathogen. Nipah virus disease is endemic in south Asia and outbreaks have been reported in Malaysia, Singapore, India, and Bangladesh. Bats of the genus Pteropus appear to be the natural reservoir of this virus. The aim of this study was to investigate the genetic diversity of Nipah virus, to estimate the date of origin and the spread of the infection. The mean value of Nipah virus N gene evolutionary rate, was 6.5 × 10−4 substitution/site/year (95% HPD: 2.3 × 10−4–1.18 × 10−3). The time‐scaled phylogenetic analysis showed that the root of the tree originated in 1947 (95% HPD: 1888–1988) as the virus entered in south eastern Asiatic regions. The segregation of sequences in two main clades (I and II) indicating that Nipah virus had two different introductions: one in 1995 (95% HPD: 1985–2002) which correspond to clade I, and the other in 1985 (95% HPD: 1971–1996) which correspond to clade II. The phylogeographic reconstruction indicated that the epidemic followed two different routes spreading to the other locations. The trade of infected pigs may have played a role in the spread of the virus. Bats of the Pteropus genus, that are able to travel to long distances, may have contributed to the spread of the infection. Negatively selected sites, statistically supported, could reflect the stability of the viral N protein. J. Med. Virol. 88:380–388, 2016. © 2015 Wiley Periodicals, Inc.