This dataset comprises genome-wide single nucleotide polymorphisms (SNPs) generated from 92 accessions of Camellia, including 87 wild germplasm accessions of Camellia sect. Eriandria and sect. Theopsis, together with five outgroup accessions from other sections, using super genotyping-by-sequencing (super-GBS). The focal sections, mostly endemic to China, possess valuable traits including fragrance, abundant flowering, and stress tolerance. The data were analyzed using population genomic and phylogenomic approaches to elucidate the genetic structure, evolutionary relationships, and taxonomic boundaries of these taxonomically challenging groups, whose classification has long been controversial because of reliance on a single morphological trait. Variant data are provided in VCF format with associated metadata, enabling further studies on the conservation and utilization of these germplasm resources.