The ability to generate conditional mutant alleles in mice using Cre‐lox technology has facilitated analysis of genes playing critical roles in multiple developmental processes at different times. We used a transgenic Hoxb6 promoter to drive tamoxifen‐dependent Cre recombinase expression in several developing systems that serve as major models for elucidating inductive interactions and mechanisms of morphogenesis, including lateral plate mesoderm and descendant limb buds, neural crest progenitors of the neural tube, tailbud, and CNS isthmic organizer. The Hoxb6CreER^T line gives very rapid and complete recombination over a short time window after a single tamoxifen dose, allowing precise time requirements for gene function to be assessed accurately. Embryonic cells cultured from the Hoxb6CreER^T line also display rapid recombination ex vivo after tamoxifen exposure. Hence, the Hoxb6CreER^T line provides a valuable tool for analyzing gene function, as well as lineage tracing studies using genetic cell marking, in several developing systems. Developmental Dynamics 238:467–474, 2009. Published 2009 Wiley‐Liss, Inc.