JE is one of the most important vector-borne viral encephalitis in East and Southeast Asian countries. Japanese encephalitis is being maintained in nature through a peridomestic cycle involving a field cycle. JEV is maintained in nature as a single serotype along with genotypes I–V (GI–GV). Geographic expansion and international travel to Asia in recent years have significantly increased the incidence of JE. JEV genotype I (GI) has replaced GIII as the dominant genotype in Asia, while GIII has started spreading to Europe and African countries with limited domestic cases. JEV GI is one of the most recent but dominant genotypes. Genotype GI existed as GI-a and GI-b clades, where GI-a prevailed in the tropical regions of Asia as Thailand subgroup and Cambodia subgroup. GI-b clade gradually replaced the GIII genotype as the dominant strain in Asia and spread northward from Vietnam through China to Japan and Korea in East Asia. GIII has been known to cause outbreaks of JE throughout Asia since 1924 in Tokyo, Japan, where 6000 JE cases with 60% mortality were reported. India witnessed an outbreak in 2005 in Gorakhpur, where 5737 patients with GIII were affected with 1344 fatalities. Although JEV GIII is predominant in temperate regions, recently, it has been isolated from non-endemic areas of Southern Europe. Importantly, changing geographical distribution and emergence of JEV genotypes are a matter of concern and need to be handled through active disease surveillance and vaccination policy. Therefore, it is requisite to strengthen monitoring of JE and its genotypes, especially in non-endemic areas. Hence, this chapter focuses on the global trends in phylogenetic genotype-based epidemiology of JEV.