Gaoligong Mountains in Yunnan Province, China have diverse ecological systems and biological resources. To understand the diversity and the vertical distribution of Metarhizium species at different elevations in this area, Metarhizium resources were investigated in seven typical vegetation types (i.e., I, dry-hot valley; II, monsoon evergreen broad-leaved forest; III, warm coniferous forest; IV, mod-montane humid evergreen broad-leaved forest; V, mountain moss dwarf forest; VI, cold shrubs of meadow; and VII, rocky beach sparsely vegetation) along an elevation gradient (600-3,800 m). Strains of Metarhizium were isolated from soils of the vegetations at different elevations and identified using multi-gene (nrSSU, nrLSU, EF-1α, RPB1, and RPB2) phylogenetic analysis. Our result indicated that the species of Metarhizium in Gaoligong Mountains were abundant and the obtained 161 strains represented 12 Metarhizium species, namely, M. rileyi, M. viridulum, M. lepidiotae, M. brunneum, M. pingshaense, M. anisopliae, M. robertsii, M. guizhouense, M. indigoticum, M. pemphigi, M. campsosterni, and Metacordyceps neogunnii, and most of them (8 species) belonged to M. anisopliae complex. Additionally, Nigelia martiale, a taxon close to Metarhizium was also found in this area. M. indigoticum is new to China. Fungi of Metarhizium in Gaoligong Mountains were widely distributed in six vegetation types at elevation between 600 m and 3,400 m, but not in type VII at the elevation of 3,600-3,800 m. The vegetations at the low and middle elevations (I-IV) harbored larger number of strains (≥ 23) and higher species diversity (4-9 species), whereas those at high elevations (V-VI) possessed fewer strains (2-8) and relatively limited species (1-2 species). Metarhizium resources were the most abundant in evergreen broad-leaved forests at the middle elevation. The monsoon evergreen broad-leaved forest (vegetation type II) possessed the largest number of Metarhizium strains (52 strains, 32.3% of the total) and species (9 species), while mid-montane humid evergreen broad-leaved forest (vegetation type IV) (47 strains, 29.2% of the total) was the next. The superior species phenomenon of Metarhizium was remarkable in Gaoligong Mountains, M. brunneum being the most dominant, at 46.6% of the total strain numbers. It widely exists in six vegetation types (I-VI) with very different habitat conditions, suggesting that this species has the highest ecologic adaptability.