Polyploid formation is a major mode of sympatric speciation in flowering plants. Unlike other speciation processes, polyploidization is often assumed to confer instant reproductive isolation. Shared polymorphism across ploidy levels has therefore often been attributed to multiple polyploid origins, whereas the alternative hypothesis of introgressive hybridization has rarely been rigorously tested. Here, we sequence 12 nuclear loci representing 6 genes duplicated by polyploidy in 92 accessions of the tetraploid Capsella bursa-pastoris together with the corresponding loci in 21 accessions of its close diploid relative Capsella rubella. In C. bursa-pastoris accessions from western Eurasia, where the 2 species occur in partial sympatry, we find higher levels of nucleotide diversity than in accessions from eastern Eurasia, where C. rubella does not grow. Furthermore, haplotypes are shared across ploidy levels at 4 loci in western but not in eastern Eurasia. We test whether haplotype sharing is due to retention of ancestral polymorphism or due to hybridization and introgression using a coalescent-based isolation-with-migration model. In western but not in eastern Eurasia, there is evidence for unidirectional gene flow from C. rubella to C. bursa-pastoris. An independent estimate of the timing of dispersal of C. bursa-pastoris to eastern Eurasia indicates that it probably predated introgression. Our results show that polyploid speciation need not result in immediate and complete reproductive isolation, that postpolyploidization hybridization and introgression can contribute significantly to genetic variation in a newly formed polyploid, and that divergence population genetic analysis constitutes a powerful way of testing hypotheses on polyploid speciation.