The recent analysis of the homologies of the elements in the highly derived pectoral girdle of turtles is used as an example to clarify how character congruence tests conjectures of homology in cladistic analysis. Character congruence does not test alternative conjectures of similarity i.e. alternative character definitions and/or descriptions. It will only test the proposition that an observed relationship of similarity is homologous or not, and hence indicate whether this observed relationship of similarity may be parsimoniously explained by common ancestry, or must rather be treated as homoplasy. To test alternative hypotheses of homology, or alternative conjectures of similarity, the data matrix must be constructed such as to allow the evaluation of these alternatives on the basis of parsimony.