The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. Pear is a relatively popular pome fruit belonging to the genus Pyrus. To examine viruses and viroids infecting pear in Korea, we collected 110 pear leaf samples from 35 orchards in five major pear producing area from June 2017 to October 2018. Nine viruses including six viruses in the family Betaflexiviridae and one viroid were identified in two different pear libraries. Most virus-associated contigs were matched to sequences of known viruses in pears, including Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), and Apple stem grooving virus (ASGV). However, some contigs were matched to sequences of Apple green crinkle associated virus (AGCaV) or Grapevine yellow speckle viroid (GYSVd), which is the first detection of the virus and viroid in pear. Phylogenetic analyses indicated that AGCaV was separated from ASPV isolates and GYSVd was grouped with 10 type 1 GYSVd isolates. Furthermore, we analyzed the amount of viral RNA and the copy number for the identified viruses and viroid. Based on the number of virus-associated reads, ASPV and ASGV were dominant viruses infecting two pear cultivars in Korea. Taken together, we describe the viral population and provide a comprehensive overview of the diversity of viral communities in two different pear cultivars.