Shox2 is expressed in several developing organs in a tissue specific manner in both mice and humans, including the heart, palate, limb, and nervous system. To better understand the spatial and temporal expression patterns of Shox2 and to systematically dissect the genetic cascade regulated by Shox2, we created Shox2‐LacZ and Shox2‐Cre knock‐in mouse lines. We show that the Shox2‐LacZ allele expresses beta‐galactosidase reporter gene in a fashion that recapitulates the endogenous Shox2 expression pattern in developing organs, including the sinoatrial node (SAN), the anterior portion of the palate, and the proximal region of the limb bud. Conditional deletion of Shox2 in mice carrying the Shox2‐Cre allele yielded SAN phenotypes that resemble conventional Shox2 knockout mice. Our results indicate that the Shox2‐Cre allele offer a useful tool for tissue specific manipulation of genes in a number of developing organs, particularly in the developing SAN. genesis 51:515–522. © 2013 Wiley Periodicals, Inc.