Asia, especially the temperate Sino-Himalayan region is one of the four major diversity centers of Indigofera. Pollen morphology of Indigofera species in the Sino-Himalayan region is poorly known. In this study, pollen morphology of 52 samples representing 43 Chinese Indigofera species and two varieties was examined using scanning electron microscopy to evaluate its taxonomic significance. Parasyncolpate pollen grains were described in Indigofera for the first time. Cluster and principal component analyses were conducted based on four quantitative and three qualitative pollen characters. Five groups were recognized within Chinese Indigofera in the cluster analysis, but only one can be separated by the first three principal components. The shape and size of pollen grains in Indigofera are highly variable. Consequently, both the characters lack any significant taxonomic value. The number of apertures, tectum architecture and perforation density shows some taxonomic significance. The pollen morphology exhibits obvious phylogenetic and biogeographical significance on large scales in Indigofera. Although pollen characters alone are insufficient to reconstruct the taxonomic relationships within Indigofera, palynological data can provide some useful information for the species-level revisions.