Human Zic2, a zinc-finger transcription factor, is strongly associated with holoprosencephaly (HPE), a malformation of the forebrain, and with a unique set of dysmorphic facial features. We have previously used knockdown assays to demonstrate critical roles for zebrafish Zic2 orthologs, Zic2a and Zic2b, in the developing retina, forebrain and craniofacial cartilages. To examine the mechanism of Zic2 function in more depth, we have generated compound zic2a;zic2b mutants and determined that embryos homozygous for mutant alleles at both zic2a and zic2b loci develop with retinal coloboma, aberrantly shaped ventricles and greatly reduced and disorganized craniofacial cartilage. In addition, mutant embryos present with periocular hemorrhages and edema suggestive of vascular malformations. To characterize the molecular consequences of Zic2 loss-of-function, we examined transcriptomes of zic2a;zic2b mutant embryos vs siblings using RNAseq. The resulting gene set identified several neural crest lineages, including but not limited to chondrogenic neural crest, as strongly dependent on Zic2 function. Among the candidate zic2 targets is a homeobox gene Alx1, which is expressed in neural crest and is required for both craniofacial and retinal morphogenesis in zebrafish. Moreover, human Alx1 has been linked to a severe form of frontonasal dysplasia. Based on these data, we hypothesize that Zic2 functions in neural crest lineages that contribute to craniofacial structures and regulate formation of adjacent structures, including the ventral retina. In-depth functional analysis of Alx1 and other candidate targets of Zic2 identified by RNA-seq will test this hypothesis, clarifying the mechanism of conserved Zic2 functions during vertebrate embryogenesis.