Аннотация:One hundred and twenty-three isolates of Botrytis cinerea were collected from 7 different areas in the Republic of Macedonia, where tomato is mostly grown in greenhouses and high tunnels. Based on the mycelial formation, intensity of sporulation and sclerotial production, 9 different phenotypes were detected: 4 mycelial and 5 sclerotial. One sclerotial morphological type has not been previously reported. The presence or absence of two transposable elements, boty and flipper, was detected by PCR. Out of 123 isolates, 20 had two transposable elements, boty and flipper (transposa genotype), 48 had neither of these elements (vacuma genotype) and 55 had only the flipper element (flipper genotype). Isolates that contain only boty element were not detected. No relationship between the phenotypes, origin of isolates and the presence/absence of transposable elements, boty and flipper, was found.