Twenty-one trilobite species belonging to 16 genera and subgenera, 11 families and seven orders are systematically documented from the uppermost Ordovician and the lowermost Silurian strata (upper Hirnantian-Rhuddanian) at three sections in north-eastern Yunnan and northern Guizhou provinces, south-west China. Together with those trilobites previously reported from the Yanping section of northern Guizhou, these trilobites constitute the earliest known recovery trilobite faunas in South China after the Late Ordovician mass extinction (LOME) and are characterized by the Silurian-type Sinoencrinurus gen. nov. and Ciliscutellum faunas. Two new genera (Sinoencrinurus gen. nov. and Yunnanoproetus gen. nov.) and four new species (Ciliscutellum rhaxerosides sp. nov., Meadowtownella yunnanensis sp. nov., Batocara tuberosus sp. nov. and Yunnanoproetus shanshuensis gen. et sp. nov.) are described. The monophyly of Sinoencrinurus gen. nov. is well supported by the results of phylogenetic analysis, and it may form a sister group to Coronocephalus. Two genera, Meadowtownella and Batocara, have their first records in South China. Supported by evidence from faunal composition, lithology and numerical analyses, six trilobite associations are recognized along environmental gradients from nearshore to inner shelf. These associations had prominent ecological differentiation and strong endemicity to South China. Their ecological differences and distribution were mainly controlled by oxygen levels, depth gradients and substrate conditions. The mode of life and environmental tolerance of different trilobite taxa may also be part of the controlling factors. https://zoobank.org/urn:lsid:zoobank.org:pub:8B5C65ED-9523-4ACD-ABD4-86EE01127975