Since molecular features such as regulatory genes create or direct the creation of anatomical features, it makes sense that these two lines of evidence would indicate the same relationships among organisms. One case in which the opposite would be found would be convergent evolution in which similar looking structures of different origins would confuse the analysis.
Work Step by Step
Review the material on homology and analogy (convergence). Also, past chapters show how molecular features help create larger scale/anatomical features, which helps answer the first part of the question.