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Incipient species often coexist in sympatry before complete reproductive isolation has evolved between them. How do they persist in the face of hybridization and gene flow? The challenge is more acute than ordinary ecological coexistence not only because gene flow erodes and recombines genetic differences, but also because selection against hybrids can destabilize population sizes. We estimated gene flow and selection against hybrid genotypes between sympatric limnetic and benthic species of threespine stickleback in two British Columbia lakes. First-generation hybrids are present at a rate of about 2%. To estimate selection, we compared the frequency distribution of ancestry proportions between juvenile and adult samples. We also used genomic simulation with assortative mating in an ecological model to determine how much selection is required to reproduce observed genotype frequencies. Results from the two approaches were comparable and yielded estimated selection coefficients S against the least fit ancestry proportion (within backcross range) between 0.5 – 0.6. Surprisingly, selection was found to be only slightly weaker than that leading readily to collapse and fusion in our simulations, suggesting that sympatric stickleback species are close to a coexistence boundary. Moderately strong selection appears to be required for coexistence with even low levels of gene flow. We suggest that larger niche differences are required to stabilize coexistence with gene flow than without gene flow. This helps to explain why successful sympatric species that hybridize often show conspicuous ecological and phenotypic differences.