Endothelial cells in the atrioventricular canal of the heart undergo an epithelial‐mesenchymal transition (EMT) to form heart valves. We surveyed an on‐line database (http://www.geisha.arizona.edu/) for clones expressed during gastrulation to identify novel EMT components. One gene, latrophilin‐2, was identified as expressed in the heart and appeared to be functional in EMT. This molecule was chosen for further examination. In situ localization showed it to be expressed in both the myocardium and endothelium. Several antisense DNA probes and an siRNA for latrophilin‐2 produced a loss of EMT in collagen gel cultures. Latrophilin‐2 is a putative G‐protein‐coupled receptor and we previously identified a pertussis toxin‐sensitive G‐protein signal transduction pathway. Microarray experiments were performed to examine whether these molecules were related. After treatment with antisense DNA against latrophilin‐2, expression of 1,385 genes and ESTs was altered. This represented approximately 12.5% of the microarray elements. In contrast, pertussis toxin altered only 103 (0.9%) elements of the array. There appears to be little overlap between the two signal transduction pathways. Latrophilin‐2 is thus a novel component of EMT and provides a new avenue for investigation of this cellular process. Developmental Dynamics 235:3213–3221, 2006. © 2006 Wiley‐Liss, Inc.