Paraqianlabeo lineatus is a newly described cyprinid fish species belonging to subfamily Labeoninae.Currently, it is only found in some tributary streams with clear water and sluggish flow along Wu-Jiang and Chishui-He rivers of the upper Yangtze River basin in China With the global climate change and the intensification of human activities, its habitat has begun to be gradually destroyed The conservation of its habitats and especially its genetic resources is urgently needed However, the available genetic data for this species is very limited Nevertheless, recent advances in next-generation sequencing technologies have dramatically increased the efficiency of molecular marker development, such as single nucleotide polymorphisms and microsatellites Here we isolated 21 polymorphic microsatellite markers from a genomic library of P lineatus using illumina paired-end sequencing and further characterized using a sample from a wild population consisting of 36 individuals The number of alleles among loci ranged from 7 to 17 and the observed and expected heterozygosities ranged from 0.056 to 1.000 (mean=0.499) and 0.599 to 0.924 (mean=0.842), respectively.The polymorphic information content (PIC) of all loci ranged from 0.506 to 0.904 (mean=0.810), indicating high levels of polymorphism.These novel microsatellite loci will be useful for population genetic studies, parentage analysis and conservation management for this new species and other labeonine fishes.