In an earlier study, we demonstrated that isolates of apple stem grooving capillovirus (ASGV) from fruit trees comprise at least two to four sequence variants that differ considerably from each other in nucleotide sequence. In order to characterize the population of sequence variants within a single tree, we applied a combination of an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) and a single-strand conformation polymorphism (SSCP) analysis of a nested asymmetric PCR product. In the SSCP analysis of the PCR products from ASGV-infected apple, Japanese pear, or European pear trees, two to four bands were detected in samples from all trees, indicating that ASGV exists as a mixture of sequence variants. The composition of sequence variants (the number of bands and their relative quantity) differed among leaf samples from different branches, showing that each sequence variant is distributed unevenly within an individual tree. The SSCP analysis of isolates after serial passage in Chenopodium quinoa plants indicated that passages changed the composition of sequence variants originally contained in ASGV isolates; i.e., some sequence variants dominated and others decreased to undetectable levels.