The present study was performed to elucidate if microbial activity, fungal abundance, and distribution ofPenicilliumandFusariumcan be used as bioindicators to characterize organically cultivated soils. The experimental approach was to study a potential long-term development following transition to organic farming at four farms that had been cultivated organically for 2, 8, 11, and 31 years, respectively. Sampling was performed four times in two crops (winter wheat and leys with a mixture of grass and leguminosae). The importance of the crop was clearly demonstrated in the form of a significantly higher microbial activity in the ley soils than in the wheat soils. However, the wheat soils yielded the most consistent results and thus seem better suited for studies of the long-term development of a bioindicator. The farms were chosen carefully in an attempt to minimize the variations that will always be present when studying different, commercially run farms. These variations are caused by differences in e.g. soil type, soil management, fertilizer practice, and crop rotation and development. Bearing this in mind, the results showed that the abundance of the mainly soil-borne penicillia was significantly higher at the ‘oldest’ organically cultivated farm than at the other localities, indicating a temporal development during later years following transition to organic farming. The abundance ofFusariumwas more variable at the genus level, but some of the species seem very promising as bioindicators, especiallyF. solaniandF. equiseti, but alsoF. culmorumandF. tabacinum.The results also indicate a temporal development in species richness ofFusariumduring the first years following transition.