Cellular interactions drive mammalian kidney development. In this study, we compared the organization and interactions between distinct progenitor (mesenchymal) cell-types that give rise to different components of the kidney, between the well-studied mouse model and the poorly studied human kidney. We observed similar microenvironment harboring progenitor types between the species, but distinct differences in gene activity within progenitor cells. This study provides a benchmark for the progenitors of the human nephrogenic niche and highlights species-variability in kidney developmental programs. The findings will help to guide, efforts to harness the cellular programs necessary to build human kidney structures in the laboratory.