Our goals for this research were to elucidate phenotypic and biochemical diversity in coriander (Coriandrum sativum L.) populations maintained at the North Central Regional Plant Introduction Station in Ames, IA, and examine relationships between amplified fragment length polymorphism (AFLP) markers and patterns of phenotypic and biochemical diversity. Phenotypic and biochemical traits were evaluated, and analyses of variance and mean comparisons were performed on the resulting data sets. Euclidean distances from phenotypic (PD) and biochemical (BD) data were estimated, and modified Rogers’ distances (RD) were estimated for 80 polymorphic AFLP markers. These data were subjected to cluster analyses (CA) and principal components analyses (PCA), to reveal patterns among populations, and to analyses of molecular variance (AMOVA) for grouping patterns from PD and BD by using the 80 polymorphic AFLP markers. Resulting phenotypic, biochemical, and molecular distance matrices were also compared by applying Mantel tests. Our results describe significant differences among populations for all the phenotypic traits, and dendrograms obtained from PD and BD revealed complex phenetic patterns, as did groups from PCA. The primary seed essential oils and nearly all fatty-acid components were identified and their abundance measured; the primary chemical constituents of corresponding PCA groups are described herein. Molecular evidence supported phenotypic and biochemical subgroups. However, variation attributed among subgroups and groups was very low (∼4–6%), while variation among populations within groups was intermediate (∼24–26%), and that within populations was large (∼69–70%), reflecting weak differentiation among subgroups and groups, which was confirmed by values for fixation indices. Phenotypic subgroups described in this study differed somewhat from previous infraspecific classifications. Weak correlations were found between the phenotypic and biochemical matrices and between the biochemical and AFLP matrices. No correlation was found between the phenotypic and AFLP matrices. These results may be related to coriander’s phenotypic plasticity, its wide range in lifecycle duration, its predominantly allogamous reproductive biology, a human-selection process focused on special traits that may be controlled by few genes, and the widespread trade of coriander seeds as a spice, which may result in dynamic, poorly differentiated molecular variation, even when phenotypic and biochemical differentiation is easily documented.