SummaryHepatitis E virus genotype 3 (HEV‐3) can lead to chronic infection in immunocompromised patients, and ribavirin is the treatment of choice. Recently, mutations in the polymerase gene have been associated with ribavirin failure but their frequency before treatment according to HEV‐3 subtypes has not been studied on a large data set. We used single‐molecule real‐time sequencing technology to sequence 115 new complete genomes of HEV‐3 infecting French patients. We analyzed phylogenetic relationships, the length of the polyproline region, and mutations in the HEV polymerase gene. Eighty‐five (74%) were in the clade HEV‐3efg, 28 (24%) in HEV‐3chi clade, and 2 (2%) in HEV‐3ra clade. Using automated partitioning of maximum likelihood phylogenetic trees, complete genomes were classified into subtypes. Polyproline region length differs within HEV‐3 clades (from 189 to 315 nt). Investigating mutations in the polymerase gene, distinct polymorphisms between HEV‐3 subtypes were found (G1634R in 95% of HEV‐3e, G1634K in 56% of HEV‐3ra, and V1479I in all HEV‐3efg, clade HEV‐3ra, and HEV‐3k strains). Subtype‐specific polymorphisms in the HEV‐3 polymerase have been identified. Our study provides new complete genome sequences of HEV‐3 that could be useful for comparing strains circulating in humans and the animal reservoir.