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Species of the fungal genus <i>Metarhizium</i> are globally distributed pathogens of arthropods, and a number of biological control products based on these fungi have been commercialized to control a variety of pest arthropods. In this study, we investigate the abundance and population structure of <i>Metarhizium</i> spp. in three land-use types—arable land, grassland, and forest—to provide detailed information on habitat selection and the factors that drive the occurrence and abundance of <i>Metarhizium</i> spp. in soil. At 10 sites of each land-use type, which are all part of the Swiss national soil-monitoring network (NABO), <i>Metarhizium</i> spp. were present at 8, 10, and 4 sites, respectively. On average, <i>Metarhizium</i> spp. were most abundant in grassland, followed by forest and then arable land; 349 <i>Metarhizium</i> isolates were collected from the 30 sites, and sequence analyses of the nuclear translation elongation factor 1α gene, as well as microsatellite-based genotyping, revealed the presence of 13 <i>Metarhizium brunneum</i>, 6 <i>Metarhizium robertsii</i>, and 3 <i>Metarhizium guizhouense</i> multilocus genotypes (MLGs). With 259 isolates, <i>M. brunneum</i> was the most abundant species, and significant differences were detected in population structures between forested and unforested sites. Among 15 environmental factors assessed, C:N ratio, basal respiration, total carbon, organic carbon, and bulk density significantly explained the variation among the <i>M. brunneum</i> populations. The information gained in this study will support the selection of best-adapted isolates as biological control agents and will provide additional criteria for the adaptation or development of new pest control strategies.