Competing phylogenetic hypotheses have become the rule in modern systematics. While the problem of incongruence between character sets has become extremely acute due to the generation of molecular data, it is by no means specific to molecular and morphological comparisons. The role of the modern systematist is to interpret incongruence between character sets and to come to some conclusion regarding a phylogenetic hypothesis of the organisms in question. Two aspects of congruence analysis are examined using the Drosophilidae as an example. The first includes the quantification of congruence and the types of phylogenetic inference that can be made from such analyses. The second aspect concerns an examination of character evolution in order to identify characters and taxa that might be contributing to incongruence in phylogenetic analysis. © 1994 Wiley-Liss, Inc.