A late Holocene pollen atlas of the Jiulongchi Wetland in the Fanjingshan National Nature Reserve (a UNESCO World Heritage Site), southwestern China, is presented to facilitate Quaternary pollen identification and palaeoecological interpretation. The pollen atlas is organized according to aperture types and sculpture patterns, covering 64 genera and 37 families from conifers, broad-leaved trees and shrubs, upland and wetland herbs. The pollen grains are illustrated with high resolution images under light microscope (LM) and/or scanning electron microscope (SEM), along with a morphological index. Most pollen types are identifiable to genus level. Taxonomic precision of pollen identification for key taxa to improve palynological and palaeoecological interpretation is discussed based on high resolution pollen morphological characteristics under SEM, including key genera of Fagaceae (Quercus, Cyclobalanopsis, and Fagus) and Pinaceae (Tsuga, Abies and Pinus). Noticeably, pollen aperture and sculpture pattern of the section Cyclobalanopsis and some species from the section Ilex overlap, thus classifying them in one ecological group is highly recommended in Quaternary pollen analysis. There are still some pollen types assigned to family level currently due to high similarity of morphology and limited modern pollen references available, therefore further modern pollen collection is highly expected for detailed comparison with fossil pollen grains to improve accurate assignments. The perspectives of improving taxonomic resolution of fossil pollen identifications in the southwestern China are also briefly noted. This study enriches Holocene pollen atlas and provides interpretation aid to Quaternary pollen analysis for the study area in southwestern China and adjacent regions.