Garlic (Allium sativum L.) has been clonally propagated for thousands of years because it does not produce seed under standard cultivation conditions. A single garlic accession frequently displays a high degree of phenotypic plasticity that is likely to be dependent upon soil type, moisture, latitude, altitude, and cultural practices. The diversity observed by collectors has occasionally led to the renaming of varieties as they are exchanged among growers and gardeners. As a result, there are numerous garlic varieties available both commercially and within the USDA National Plant Germplasm System (NPGS) that may be identical genotypically, yet have unique cultivar names. To address this possibility, we performed amplified fragment-length polymorphism (AFLP) analysis on a comprehensive selection of 211 Allium sativum and Allium longicuspis accessions from NPGS and commercial sources. We used several statistical approaches to evaluate how these clonal lineages are genetically differentiated and how these patterns of differentiation correspond to recognized phenotypic classifications. These data suggest that while there are extensive duplications within the surveyed accessions, parsimony and distance based analyses reveal substantial diversity that is largely consistent with major phenotypic classes.