Embryonic levels of retinoic acid (RA) and the response of cells to RA are critical to the normal development of vertebrates. To understand the effects of RA signaling in Fundulus heteroclitus, we exposed embryos to a range of RA concentrations of 2 h during gastrulation. Embryos exposed to low concentrations of RA (10(-10)-10(-7) M) develop normally, whereas those exposed to higher concentrations (5 x 10(-7)-10(-4) M) develop characteristic dose-dependent defects. We describe, in detail, four stages of development that represent morphological effects of RA on (1) cell death and defects in the brain, heart, and eye, (2) relative size and differentiation, (3) duplications of pectoral fins, and (4) deletions in craniofacial cartilage elements. Analysis of cartilaginous skeletal elements demonstrates distinct patterns of deletions in the neurocranium and pharyngeal skeleton in response to increasing concentrations of RA. In F. heteroclitus, RA treatment during gastrulation results in five highly consistent phenotypes, which we have incorporated into an index of embryonic RA defects. This index should be valuable in the genetic analysis of RA pathways and in evaluating chemicals that interfere with embryonic RA signaling.