The melon thrips, Thrips palmi Karny, is an economically important pest on many vegetables from Solanaceae and Cucurbitaceae. In this study, we developed novel microsatellite markers for Thrips palmi. First, we obtained randomly sequenced regions from the genome using next-generation sequencing and assembled 356 Mb genomic sequences. In total, 155,789 microsatellites were identified from the genomic sequences, of which, 64.02% were loci of dinucleotide repeat. Sixty primer pairs were initially validated in seven individuals. Thirty-five polymorphic markers were retained according to the amplification efficiency and polymorphism. These 35 microsatellite loci were then assessed in 96 individuals in four geographical populations collected from China. The allele numbers ranged from 2 to 19 with an average value of 6.9 per locus, while the polymorphism information content ranged from 0.2219 to 0.8490. The observed and expected heterozygosity varied from 0.5252 to 0.5367 and 0.5934 to 0.6148, respectively. Genetic structure was found between populations from southern and northern China. These novel microsatellite markers developed in our study provide abundant molecular markers for the genetic study of T. palmi.