Numerous fish microremains, including diverse chondrichthyans, have been recovered for the first time in the Carboniferous–lower Permian of the Naqing, Narao, and Shanglong deep-water sections from Guizhou Province, South China, as well as in the Serpukhovian–lower Bashkirian of the Sholaksay section from Kazakhstan. The richest assemblage was found in the Bashkirian strata of the three South China sections. These findings are the first reliable record of Pennsylvanian fishes in China. The fish assemblage from the Sholaksay section and the Bashkirian of China closely resemble those from the same interval in the Aksu section, Uzbekistan. All studied fish faunas from these three Asian regions are associated with the Paleotethys. Notably, while Bashkirian chondrichthyan faunas generally exhibit low taxonomical diversity in many regions of the world, the deep-water fish assemblages from South China, Kazakhstan, and Uzbekistan are characterized by high taxonomical diversity. The fish fauna includes widely distributed chondrichthyan taxa; however, Gissarodus occurs only in these three Asian regions. Fishes, one of the most diverse taxa in the modern water ecosystem, underwent various morphological evolutions during the Phanerozoic. Cartilaginous and bony fishes are the two major groups of fishes. The microremians (teeth, scales, and spines) were the key to understanding the evolution process of fishes. However, the microremians of cartilaginous and bony fishes of the Carboniferous time are less known compared with other fossil groups of invertebrates, especially in China. Here we report Carboniferous deep-water fish assemblages from South China and Western Kazakhstan for the first time. A high diversity of fish fauna was found from the Bashkirian strata in both areas, while low diversity existed in most of other areas during the Early Pennsylvanian time. These findings will increase our understanding of the Carboniferous fishes.