A 3-­year retrospective study was performed based on virological surveillance data of measles virus in Shanghai from 2012 to 2014. Vero/Slam cell line was chosen to isolate virus of throat swabs collected from suspected measles cases. The fragment of C­terminal of nucleoprotein was amplified by reverse transcriptase­polymerase chain reaction (RT-­PCR), and the products were directly sequenced. The phylogenetic analysis of gene relationship was performed based on the 450 nucleotides of C­terminal of nucleoprotein. A total of 710 measles virus strains were isolated from 2 562 throat swab specimens (27.71%). Almost all the isolates were subgenotype H1a, except 1 genotype D8 and 8 genotype B3. The identity of subgenotype H1a strains was 96.0%­-98.0% for nucleotide sequence and 92.7%-­98.0% for amino acid sequence respectively when compared with a World Health Organization (WHO) representative reference strain (GenBank No. AF045212). Whereas the nucleotide sequence identity and amino acid sequence identity between genotype D8 and WHO representative reference strain (GenBank No. AF280803) and between genotype B3 and WHO representative reference strain (GenBank No. L46753) were 97.8%, 98.6% and 96.7%-­96.9%, 95.3%, respectively. The results suggest that subgenotype H1a measles virus is predominant in Shanghai from 2012 to 2014. Imported genotype D8 and B3 measles virus strains are first found in Mainland China through Shanghai measles surveillance system.