Diversification in Amelanchier tetraploid apomicts differs from that of diploid sexuals and produces groups that are taxonomically difficult. Apomixis facilitates expansion of ecologically successful genotypes into numerous, narrowly distributed, and often minimally distinct microspecies. Residual sexuality in tetraploids creates hybrid swarms and intergradation of taxa. This gene flow is evident in DNA sequences from nuclear and chloroplast regions that record mostly allotetraploid, convoluted histories. Ongoing apomixis in successful tetraploid genotypes fosters their expansion into geographically widespread phenotypic clusters. We delimit such clusters as species and deny species status to microspecies. We demonstrate polyploid complexity and our approach to species delimitation in three taxa of Amelanchier. The tetraploid microspecies A. “rubra” of southeastern Maine, while morphologically distinct, hybridizes with sympatric congeners. Eastern North American A. bartramiana contains diploids and polyploids (tetraploids and a few triploids) that are sometimes morphologically semi-cryptic. We group all ploidy levels in the A. bartramiana agamic complex and recognize as a species the diploid (A. bartramiana). The tetraploid is not given species status because it intergrades extensively with tetraploid congeners, as exemplified by the nothospecies named here, A. × neglecta . Western North American A. cusickii is tetraploid, mostly distinct morphologically and ecologically, distinct genetically, and merits species status.