Genomic heterogeneity of divergence between hybridizing species may reflect heterogeneity of introgression, but also processes unrelated to hybridization. Heterogeneous introgression and its repeatability can be directly tested in natural hybrid zones by examining multiple transects. Here, we studied hybrid zones between the European newts: Lissotriton montandoni and two lineages of L. vulgaris, with replicate transects within each zone. Over 1000 nuclear genes located on a linkage map and mtDNA were investigated using geographic and genomic clines. Overall, the five transects were all similar, showing hallmarks of strong reproductive isolation: bimodal distribution of genotypes in central populations and narrow allele frequency clines. However, the extent of introgression differed between the zones, likely as a consequence of their different ages, indicated by the analysis of heterozygosity runs in diagnostic markers. In three transects genomic signatures of small-scale (ca. 2 km) zone movements were detected. We found a limited overlap of cline outliers between transects, and no evidence of stronger differentiation between zones than between transects within zones. Introgression was heterogeneous across linkage groups, with patterns of heterogeneity similar between transects and zones. Predefined candidates for increased or reduced introgression exhibited only a subtle tendency in the expected direction, suggesting that interspecific differentiation is not a reliable indicator for the strength of introgression. These hierarchically sampled hybrid zones of different ages show how introgression unfolds with time and offer an excellent opportunity to dissect the dynamics of hybridization and architecture of reproductive isolation at advanced stages of speciation.