Allium amplectens (Alliaceae) occurs from southern California to southwestern British Columbia. I used nucleotide sequences from the chloroplast trnT-L intergenic spacer to investigate geographic patterns and phylogenetic relationships among ploidy levels in this species. Hexaploids (2n = 42) and diploids (2n = 14) were the rarest cytotypes (1.5% and 11.3% respectively), followed by tetraploids (2n = 28; 39.1%) and triploids (2n = 21; 48.1%). Phylogenetic analysis indicated that polyploids evolved from diploids at least twice, and that transitions among polyploids occurred at least six times. Abundant triploids in this species may facilitate tetraploid formation via the `triploid bridge'. Chromosomal variation and cpDNA haplotype diversity were highest in California. Nested Clade Phylogeographic Analysis indicated range expansion northward from California in two of three cpDNA clades, with subsequent range contraction and fragmentation. In British Columbia, where A. amplectens is considered at risk, two distinct morphological variants (3x and 4x respectively) were found.