Expression domains of developmental genes can indicate body part homologies between distantly related animals and give insights into interesting evolutionary questions. Two of the chief criteria for recognizing homologies are relative position with respect to surrounding body parts and special quality (for instance, a vertebrate testis, regardless of its location, is recognizable by its seminiferous cysts or tubules). When overall body plans of two animals are relatively similar, as for amphioxus versus vertebrates, body part homologies can be supported by developmental gene expression domains, which have properties of special quality and relative position. With expression patterns of AmphiNk2-l and AmphiPax2/5/8, we reexamine the proposed homology between the amphioxus endostyle and the vertebrate thyroid gland, and a previously good homology is made better. When body plans of animals are disparate, body part homologies supported by molecular genetic data are less convincing, because the criterion of relative position of gene expression domains becomes uncertain. Thus, when expression of amphioxus AmphiBMP2/4 is used to compare the dorsoventral axis between amphioxus and other animals, a comparison between amphioxus and vertebrates is more convincing than comparison between amphioxus and other invertebrates with disparate body plans. In spite of this difficulty, the use of developmental genetic evidence comparing animals with disparate body plans is currently putting the big picture of evolution into new perspective. For example, some molecular geneticists are now suggesting that the last common ancestor of all bilaterian animals might have been more annelid-like than flatworm-like.