Polyploidy is a common mode of speciation in plants. Especially in allopolyploids, the unity of two sets of genomes may provide a great opportunity for new lineages to explore vacant niches. We studied the role of polyploidization in the diversification process of the genus Cardamine. The genus contains more than two hundred species and is one of the most diversified genera in Brassicaceae. The genus is ecologically unique because it expanded habitats near to the water, and we found that many polyploid species inhabit in the spectra of niches along a upland-waterlogged gradient. Phylogenetic analysis indicated that the adaptation to the waterlogged environments occurred once in the diploid diversification. This allowed us to distinguish two groups of diploids, i.e. ‘wet’ and ‘upland’ groups. Identification of parental diploids suggested that many polyploids have hybrid origins between wet and upland groups, and we named these polyploids as ‘inter-niche allopolyplids'. To test whether the inter-niche allopolyplids have wider potential niches compared with diploid parents, we conducted a series of growth experiments in a gradient of water levels. In Cardamine, inter-niche allopolyploids are likely to be more successful than intra-niche polyploids and autopoluploids, and the pattern may explain rapid adaptation and diversification of the genus.