Well-preserved and diversified spores, cryptospores, and acritarchs have been recorded from a relatively continuous sequence that encompasses the Silurian–Devonian boundary in Qujing, Yunnan, southwest China. Four spore assemblage zones from Late Silurian to Early Devonian in age are proposed based on the first appearance datum (FAD) of characteristic spore species. In ascending stratigraphic order, they are Ambitisporites dilutus–Apiculiretusispora synorea (DS; Late Ludfordian to Early Pridoli), Synorisporites verrucatus–Apiculiretusispora plicata (VP; Pridoli), Apiculiretusispora minuta–Leiotriletes ornatus (MO; Lochkovian), and Verrucosisporites polygonalis–Dibolisporites wetteldorfensis (PW; Pragian). The acritarch assemblage from the upper part of the Yulongsi Formation, the Xiaxishancun Formation, and the lower–middle parts of the Xitun Formation indicates an age of Late Silurian. Based on palynological evidence, the upper part of the Yulongsi Formation is considered Late Ludfordian to Early Pridoli in age; the Xiaxishancun Formation is believed to be Pridoli in age; the Xitun Formation is considered Late Pridoli to Early Lochkovian in age; the Guijiatun Formation is considered Lochkovian in age; and the Xujiachong Formation is Late Lochkovian to Pragian in age. The Silurian-Devonian boundary is recognized between the VP and the MO spore biozones, and occurs within the middle part of the Xitun Formation.