The source of European-type subgenotype 3e/3sp hepatitis E virus (HEV) strain that is prevalent in hepatitis E patients in Mie, Japan, remained unknown. The present analyses of stored RNA samples that had been extracted from liver tissues obtained from 85 slaughtered pigs in Mie in 2007, revealed the presence of two HEV strains (swJ-Mie07-37L and swJ-Mie07-80L). The swJ-Mie07-80L strain was classified into subgenotype 3b/3jp, while swJ-Mie07-37L belonged to 3e/3sp and shared high nucleotide sequence identities of 98.3-99.2% with the 3e/3sp strains recovered from hepatitis E patients in Mie during 2004-2012. These results suggest that pigs are important reservoirs for HEV infection even in Mie, although the hepatitis E patients did not recall consuming raw pig liver/intestine before the disease onset.