A total of 55 Botrytis cinerea isolates collected from Pinus radiata and Eucalyptus globulus plants cultivated in nurseries located in the Bio-Bio Region, Chile, as well as isolates collected from native plants such as Rubus spp and Aristotelia chilensis located near the nurseries were genetically characterized. All isolates carried the Bc-hch2 allele, thus belonging to genetic Group II, which is now referred to as B.cinerea. Genotyping based on the presence of transposons Boty and Flipper showed differences between isolates related to the plant host. Thus, transposa isolates (containing both transposons) were detected in P.radiata and E.globulus, while vacuma isolates (containing neither transposon) were detected in all plants except E.globulus. Notably, boty isolates (containing just the Boty transposon) were detected at high frequencies in all plant hosts. Analyses to detect mutations involved in resistance to fungicides such as benzimidazoles (BZ), dicarboximides and QoIs also showed differences in the studied isolates. Isolates collected from E.globulus were shown to carry mutations for all tree fungicides, while those collected from P.radiata presented mutations involved in resistance to BZ only. Isolates collected from native plant hosts did not carry any of the mutations analysed.