Damaged and immature specimens often result in macroinvertebrate data that contain ambiguous parent-child pairs (i.e., abundances associated with multiple related levels of the taxonomic hierarchy such as Baetis pluto and the associated ambiguous parent Baetis sp.). The choice of method used to resolve ambiguous parent-child pairs may have a very large effect on the characterization of invertebrate assemblages and the interpretation of responses to environmental change because very large proportions of taxa richness (73-78%) and abundance (79-91%) can be associated with ambiguous parents. To address this issue, we examined 16 variations of 4 basic methods for resolving ambiguous taxa: RPKC (remove parent, keep child), MCWP (merge child with parent), RPMC (remove parent or merge child with parent depending on their abundances), and DPAC (distribute parents among children). The choice of method strongly affected assemblage structure, assemblage characteristics (e.g., metrics), and the ability to detect responses along environmental (urbanization) gradients. All methods except MCWP produced acceptable results when used consistently within a study. However, the assemblage characteristics (e.g., values of assemblage metrics) differed widely depending on the method used, and data should not be combined unless the methods used to resolve ambiguous taxa are well documented and are known to be comparable. The suitability of the methods was evaluated and compared on the basis of 13 criteria that considered conservation of taxa richness and abundance, consistency among samples, methods, and studies, and effects on the interpretation of the data. Methods RPMC and DPAC had the highest suitability scores regardless of whether ambiguous taxa were resolved for each sample separately or for a group of samples. Method MCWP gave consistently poor results. Methods MCWP and DPAC approximate the use of familylevel identifications and operational taxonomic units (OTU), respectively. Our results suggest that restricting identifications to the family level is not a good method of resolving ambiguous taxa, whereas generating OTUs works well provided that documentation issues are addressed.