Characterization of cuticular hydrocarbons permits basic distinctions among colonies of Solenopsis invicta Buren, Solenopsis richteri Forel and their hybrids (Hymenoptera: Formicidae); thus, providing opportunities to investigate details of landscape ecology for this species complex and to assess levels of invasiveness. We introduce an alternative method for the cluster analysis of cuticular molecules of imported fire ants that is complementary to a widely-used method based on calculating cuticular hydrocarbon and venom alkaloid indices. Results from this GC-MS method were analyzed using various hierarchical and normal mixtures clustering methods to test the stability of group membership. Principal component and discriminant analyses were used to produce three-dimensional views of group separation. The relative proportions of 12 intensity peaks served to differentiate imported fire ant hybrids into four assemblages – hybrids closely allied with S. invicta, hybrids close to S. richteri, a ‘core’ hybrid grouping, and an ‘outlier’ hybrid group. The most influential peaks of the assemblage (based on F-values) included 3 peaks with the piperidine structural motif and an alkane. Use of 3 peaks identified by stepwise linear discriminant analysis resulted in misclassification of 5% of the ant colonies, whereas use of 4 peaks resulted in the misclassification of 2.5%. Thus, this GC-MS method and multivariate assessment of biochemical data may facilitate the finer-scale distinction of hybrid colonies in terms of their surficial semiochemical complexity and ‘alliance’ with parental species. Application of these techniques would be especially useful in refining biological control strategies.