Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole genome sequence data supported secondary contact after a period of allopatry. This period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. Furthermore, differentiation was elevated at regions where chromosomes are inverted between species. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum.