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Background  Rivers and streams facilitate movement of individuals and their genes across the landscape and are generally recognized as dispersal corridors for riparian plants. Nevertheless, some authors have reported directly contrasting results, which may be attributed to a complex mixture of factors, such as the mating system and dispersal mechanisms of propagules (seed and pollen), that make it difficult to predict the genetic diversity and population structure of riparian species. Here, we investigated a riparian self-fertilizing herb  Caulokaempferia coenobialis , which does not use anemochory or zoochory for seed dispersal; such studies could contribute to an improved understanding of the effect of rivers or streams on population genetic diversity and structure in riparian plants. Using polymorphic ISSR and cpDNA loci, we studied the effect at a microgeographic scale of different stream systems (a linear stream, a dendritic stream, and complex transverse hydrological system) in subtropical monsoon forest on the genetic structure and connectivity of  C. coenobialis  populations across Dinghu Mountain (DH) and Nankun Mountain (NK).    Results  The results indicate that the most recent haplotypes (DH: H7, H8; NK: h6, h7, h11, h12) are not shared among local populations of  C. coenobialis  within each stream system. Furthermore, downstream local populations do not accumulate genetic diversity, whether in the linear streamside local populations across DH ( H : 0.091 vs 0.136) or the dendritic streamside local populations across NK ( H : 0.079 vs 0.112, 0.110). Our results show that the connectivity of local  C. coenobialis  populations across DH and NK can be attributed to historical gene flows, resulting in a lack of spatial genetic structure, despite self-fertilization. Selfing  C. coenobialis  can maintain high genetic diversity ( H  = 0.251;  I  = 0.382) through genetic differentiation ( G  ST  = 0.5915;  F  ST  = 0.663), which is intensified by local adaptation and neutral mutation and/or genetic drift in local populations at a microgeographic scale.    Conclusion  We suggest that streams are not acting as corridors for dispersal of  C. coenobialis , and conservation strategies for maintaining genetic diversity of selfing species should be focused on the protection of all habitat types, especially isolated fragments in ecosystem processes.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03101-7.

bmc plant biology

Population genetic structure and connectivity of a riparian selfing herb Caulokaempferia coenobialis at a fine-scale geographic level in subtropical monsoon forest