Abstract Strawberry runners are a high-value cash crop in Spain that requires vigorous transplants free of pathogens. Pre-plant soil fumigation with methyl bromide (MB), or with mixtures of MB and chloropicrin (Pic), are standard practices for controlling soil-borne diseases. However, use of MB will be forbidden in European Union countries by the year 2005; for this reason several soil fumigants have been tested as chemical alternatives to MB in Spanish strawberry nurseries. Because of the known broad activity of these compounds, their effects on strawberry soil fungal communities were studied. Experiments were conducted over a 5-year period, with pre-plant applications at two different locations each year. Soil fungal populations were estimated in each plot before and after treatments on potato-dextrose agar amended with 0.5 g l −1 streptomycin sulphate and selective media for Fusarium spp., Pythium spp., Verticillium spp., Phytophthora spp., and Rhizoctonia spp. Soil fungal populations in Spanish strawberry nurseries were clearly reduced in number and composition after pre-plant soil fumigation. Differences in the level of reduction was obtained with some treatments. Penicillium sp., following by Alternaria sp., Fusarium sp., Morteriella sp., Cladosporium sp. , Pythium sp., and Verticillium spp. were usually presented in Spanish nursery soils from March to April, whereas Phytophthora spp. and Rhizoctonia spp. were only sporadically isolated. All the fumigants reduced the soil fungal population quantitatively, but only MB:Pic and dazomet caused a clear change in their fungal genera composition. A total reduction was observed on Pythium and Morteriella populations after application of all the fumigants, except for DMDS. Populations of Verticillium spp. were also reduced by the applied fumigants in the strawberry nursery soils tested; the lowest reductions were obtained with 1,3-D:Pic + Virtually Impermeable Film, metam sodium, metam potassium and DMDS.