We examined the brain expression patterns of zebrafish genes Lhx6, Lhx7, Dlx2a, GAD67, and Tbr2/eomesa; except for GAD67, expression domains are restricted to the forebrain. In particular, a distribution of transcripts in the early zebrafish telencephalon comparable to that of tetrapods is revealed. Expression domains of Lhx6 and Lhx7 are restricted to a ventral subdivision (Sdv) of the precommissural dorsal subpallium, interpreted here as the homologue of the mammalian medial ganglionic eminence (the adult pallidum in mammals). In contrast, there is no such expression in the dorsal subdivision (Sdd) of the dorsal subpallium, interpreted here as the homologue of the mammalian lateral ganglionic eminence (the adult caudatoputamen in mammals). The Lhx6 and Lhx7 genes are furthermore expressed in the zebrafish ventral subpallium (Sv, septum), and in the supra-/postcommissurally lying posterior subdivision of the dorsal subpallium (Sdp; possible homologue of the subpallial amygdala). Also in support of this comparative interpretation, Dlx2a is generally expressed in all of the subpallium, including the ventricular zones of (all three subvidisions of) the dorsal as well as of the ventral subpallium. In contrast, Tbr2 is expressed in all of the zebrafish pallium and in a restricted zone of the ventral subpallium, comparable to the known restricted septal expression in mammals. The telencephalic expression of GAD67 largely coincides with that of Dlx2a. However, GAD67-positive cells migrate (radially) into postmitotic zones of the peripheral subpallium (as does Dlx2a and Lhx6) as well as (tangentially) into pallial zones (as does Dlx2a, but not Lhx6). J. Comp. Neurol. 507:1245–1257, 2008. © 2008 Wiley-Liss, Inc.