Kidney development is distinguished by the sequential formation of three structures of putatively equivalent function from the intermediate mesoderm, the pronephros, mesonephros, and metanephros. While these organs differ morphologically, their basic structural organization exhibits important similarities. The earliest form of the kidney, the pronephros, is the primary blood filtration and osmoregulatory organ of fish and amphibian larvae. Simple organization and rapid formation render the Xenopus pronephric kidney an ideal model for research on the molecular and cellular mechanisms dictating early kidney organogenesis. A prerequisite for this is the identification of genes critical for pronephric kidney development. This review describes the emerging framework of genes that act to establish the basic components of the pronephric kidney: the corpuscle, tubules, and the duct. Systematic analysis of marker gene expression, in temporal and spatial resolution, has begun to reveal the molecular anatomy underlying pronephric kidney development. Furthermore, the emerging evidence indicates extensive conservation of gene expression between pronephric and metanephric kidneys, underscoring the importance of the Xenopus pronephric kidney as a simple model for nephrogenesis. Given that Xenopus embryos allow for easy testing of gene function, the pathways that direct cell fate decisions in the intermediate mesoderm to make the diverse spectrum of cell types of the pronephric kidney may become unraveled in the future.