Natural rubber is an important biopolymer utilized in more than 4,000 commercial products. Nevertheless, the accumulation of waste rubber poses a significant environmental challenge due to its resistance to natural degradation. The present study sought to isolate and identify fungi from discarded rubber materials and assess their potential involvement in the early-stage surface deterioration of natural rubber. An initial screening of 69 fungal strains for extracellular enzyme production, including esterases, lipases, proteases, and laccases, was conducted. Following preliminary qualitative assays, 36 enzyme-producing isolates were further assessed for their capacity to modify natural rubber using rubber disc assays. Four isolates (L-12A, L-25, L-33, and T-21) showed measurable surface alterations associated with early-stage deterioration, as evidenced by limited mass loss, positive Schiff's reagent staining, and surface alterations observed through scanning electron microscopy (SEM). After 2 months of incubation, rubber mass loss ranged from 0.77% ± 0.27% to 1.24% ± 0.25%. Schiff's reagent staining indicated oxidative modification of the rubber surface, and SEM analysis revealed surface cracking, erosion-like features, and fungal colonization. Combined morphological characteristics and multilocus phylogenetic analyses identified these strains as Neocosmospora bostrycoides (L-12A), Neocosmospora sp. (T-21), Paracremonium laticis (L-25), and Schizophyllum commune (L-33). Descriptions, illustrations, and phylogenetic analyses of the four species are presented. This study provides preliminary evidence that these fungi may contribute to early-stage surface deterioration and oxidative modification of natural rubber.