A new species of inquiline gall wasp, Synergus nanlingensis Wang & Zeng, sp. nov., which was reared from galls on Castanopsis eyrei Tutch (Fagaceae) collected in Guangdong Province, China, is described and illustrated herein along with its mitochondrial genome. The mitogenome of S. nanlingensis is 16,604 base pairs in length and comprises 37 genes, which is typical of mitogenomes. One large control region was detected in the S. nanlingensis mitogenome, which differed from that reported for other Cynipidae species. Similar to other Cynipidae species, S. nanlingensis has the same four common gene rearrangement events; however, it shows some differences, as follows: trnS1 is downstream of Cytb; trnS2 is upstream of nad1; and trnC is downstream of rrnS. Phylogenetic analysis using COI, CytB, and 28S-D2 sequences confirmed that S. nanlingensis is a distinct species belonging to the genus Synergus Hartig.