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Background  The Gesneriaceae genus  Chiritopsis , confined almost exclusively to cave or cave-like microhabitats of limestone karsts of southern China, was described to distinguish it from  Chirita  by much smaller flowers and generally miniature plant sizes in the former genus. However, molecular phylogenetic analyses showed that  Chiritopsis  is polyphyletic and its species delimitation has been problematic. To understand how many times Chiritopsis-like species have evolved from within the recircumscribed  Primulina  and to further clarify their species identification, we sampled all but two recently described species of Chiritopsis-like  Primulina  and reconstructed their phylogenetic relationship based on DNA sequences of nuclear ITS and chloroplast  trnL - F  and  trnH - psbA .    Results  With 182 accessions of 165 taxa of  Primulina  sampled, our analyses placed the 40 accessions of 25 taxa of Chiritopsis-like  Primulina  in 17 unrelated positions, indicating at least 17 independent origins of the traits associated with caves or cave-like microhabitats. Of the 17 clades containing Chiritopsis-like  Primulina , Clade 1 is composed of  P. bipinnatifida ,  P. cangwuensis ,  P. jianghuaensis ,  P. lingchuanensis , and  P. zhoui , as well as additional samples that show variable and overlapping morphology in leaf shapes. Clade 10 includes  P. cordifolia ,  P. huangii , and  P. repanda , while  Primulina repanda  var.  guilinensis  is not placed within Clade 10.  Primulina glandulosa  var.  yangshuoensis  is not placed in the same clade of  P. glandulosa .    Conclusions  Based on our data,  P. cangwuensis ,  P. jianghuaensis , and  P. lingchuanensis  are proposed to synonymize under  P. bipinnatifida , with  P. zhoui  treated as a variety of  P. bipinnatifida .  Primulina repanda  var.  guilinensis  is transferred as  P. subulata  var.  guilinensis  comb. nov. and  Primulina pseudoglandulosa  nom. nov. is proposed for  P. glandulosa  var.  yangshuoensis . One new species is named  P. chingipengii  to honor the late Dr. Ching-I Peng (1950–2018).    Electronic supplementary material  The online version of this article (10.1186/s40529-019-0266-x) contains supplementary material, which is available to authorized users.

Molecular systematics of Chiritopsis-like Primulina (Gesneriaceae): one new species, one new name, two new combinations, and new synonyms