Cultivation-independent analyses of fungi are used for community profiling as well as identification of specific strains in environmental samples. The objective of the present study was to adapt genotyping based on simple sequence repeat (SSR) marker detection for use in cultivation-independent monitoring of fungal species or strains in bulk soil DNA. As a model system, a fungal biocontrol agent (BCA) based on Beauveria brongniartii, for which six SSR markers have been developed, was used. Species specificity of SSR detection was verified with 15 fungal species. Real-time PCR was used to adjust for different detection sensitivities of the six SSR markers as well as for different template quantities. The limit for reliable detection per PCR assay was below 2 pg target DNA, corresponding to an estimated 45 genome copies of B. brongniartii. The cultivation-independent approach was compared to cultivationdependent SSR analysis with soil samples from a B. brongniartii BCA-treated field plot. Results of the cultivationindependent method were consistent with cultivation-dependent genotyping and allowed for unambiguous identification and differentiation of the applied as well as indigenous strains in the samples. Due to the larger quantities of soil used for cultivation-dependent analysis, its sensitivity was higher, but cultivation-independent SSR genotyping was much faster. Therefore, cultivation-independent monitoring of B. brongniartii based on multiple SSR markers represents a rapid and strain-specific approach. This strategy may also be applicable to other fungal species or strains for which SSR markers have been developed.Characterization and monitoring of fungi in the environment are important aspects for many research questions in fungal biology and ecology. These include, for example, characterization of fungal population structures (5, 44), investigations of fungal functions in ecosystems (34) or natural occurrence of specified fungal groups, e.g., entomopathogenic fungi (33), and studies of survival, spread, and persistence of fungal strains released to the environment (4, 16). Traditionally, identification and characterization of fungi has relied on cultivation, followed by morphological (26), biochemical (35, 40), or molecular (15) analyses. However, the cultivation step required makes these approaches both laborious and time-consuming.