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Background    Niviventer  is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of  Niviventer  in China and neighboring northern Vietnam, including topotypes of the most reported species ( n  = 6), subspecies ( n  = 8), and synonyms ( n  = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species.    Results  Our phylogeny was finely resolved, especially for the  N. confucianus -like species. Our data provided the first support for  N. brahma  and  N. eha  as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of  N. confucianus  and one of  N. fulvescens  were supported as genetically distinct in our species delimitation analyses, while three recognized species ( N. coninga ,  N. huang , and  N. lotipes ) were not strongly supported as distinct.    Conclusions  Our results suggested that several genetically distinct species may be contained within the species currently known as  N. confucianus  and  N. fulvescens . In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for  N. coninga ,  N. huang , and  N. lotipes  indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0832-8) contains supplementary material, which is available to authorized users.

Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China