The African fig fly, Zaprionus indianus Gupta (Diptera: Drosophilidae), is an ecologically diverse pest species that interacts with and feeds on various microbial pathogens including bacteria and yeast found in decomposing fruits. However, the interaction of Z. indianus with its microbial community and microbial pathogens is obscure. To determine the presence of fungal pathogens, we collected wild Z. indianus from the northwestern part of the Indian subcontinent. Based on molecular identification and phylogenetic analysis, Debaryomyces hansenii (Zopf) Lodder & Kreger‐van Rij (isolate ziha1) was the most commonly observed fungus associated with Z. indianus. Furthermore, we identified two more opportunistic fungal pathogens: Aspergillus flavus Link (isolate zias2), and Pichia kudriavzevii Boidin, Pignal & Besson (isolate zibd3). The interaction of isolated fungi with Z. indianus was evaluated in terms of larval mortality, adult emergence, and fecundity. Debaryomyces hansenii ziha1 resulted in 90% emergence rate for adults, and did not cause significant mortality in the larval stage. In contrast, A. flavus zias2 and P. kudriavzevii zibd3 showed a significant reduction in fecundity and caused 99% and 74% larval mortality of Z. indianus, respectively. In the laboratory oviposition preference assay, mated females of Z. indianus preferred D. hansenii ziha1 supplemented food with a positive oviposition index compared to the uninfected control and compared to food infected with P. kudriavzevii zibd3 or A. flavus zias2. These findings underscore Z. indianus' potential to act as a reservoir for both symbiotic and pathogenic fungal species, some of which may be further harnessed for effective fruit fly pest control strategies.