Experiments designed to study the variation of diversity of pathogenic fungi occurring in fibre flax agrocenosis during the growing season were conducted at the Lithuanian Institute of Agriculture Upytė Experimental Station during 1999–2002. The Upytė Experimental Station is situated in Central Lithuania. Phytopathological analyses of seed, soil and plants were done at the laboratory of the Upytė Experimental Station as well as at the Biodestructor Research Laboratory of the Institute of Botany. There were identified in the rhizosphere 9 fungal species belonging to 9 genera. On flax seedlings were identified fungi belonging to 13 genera. On flax leaves at green maturity stage was identified only Oidium lini. On flax stems at green maturity stage were identified fungi belonging to 12 genera. On mature flax stems were found fungi belonging to 15 genera. On flax seed during the experimental years were identified fungi belonging to 16 genera. The number of fungi identified on seeds varied each year, depending on the year’s weather conditions during the seed ripening period. Having summarised the results, we can assert that pathogenic fungi Fusarium spp. and Colletotrichum lini, were found both on seed and plant vegetative parts during the whole assessment period. Species composition of fungi present on seed differed depending on the weather conditions. A larger number and more diverse species were found on the seed that ripened during the years with wet growing seasons (2000 and 2001) whereas the seed that ripened during dry growing seasons (1999 and 2002) was less infected with fungi. The spread of fungi on stems and leaves was also determined by the weather conditions. Many species of fungi were identified in 2001, when flax crops were lodged; stems and capsules were damaged by hail, and in 2000, when there was much rainfall.