This study (conducted in western Poland) was aimed at recognizing the importance of straw heaps (SH) and manure heaps (MH) located in cultivated fields for fungal diversity in farmland. Fungi (24 species and 1 sterile form) were found in 19.1% of SH (N = 89) and 60.4% of MH (N = 169). The estimated species richness (Chao2) was 29.8 ± 12.7 and 18.1 ± 2.5 (SD), respectively. Species composition of fungal communities differed significantly between SH and MH. The studied ephemeral habitats contributed markedly to fungal diversity, both locally and on the national scale. The occurrence of fungi in SH was significantly positively related to heap size, while fungal species number in MH depended most strongly on the degree of shielding, linked with proximity of woods or shelterbelts. The results show that both the reduction of SH and MH numbers in farmlands (required by the Nitrates Directive) and landscape simplification are unfavorable for fungal diversity.