This chapter discusses microbiology and morphogenesis of columnar stromatolites from hot springs in Yellowstone national Park. The hot springs of Yellowstone National Park in Wyoming constitute an environment that, in some ways, is analogous to Precambrian marine environments. The great amount of microbiological data on the Yellowstone springs provides an excellent opportunity to study in depth the microbiology of columnar stromatolites. Field observations and laboratory experiments strongly suggest that the morphology and microstructure of the Conophyton stromatolites result from the phototaxis and cohesion of the principal constructing microorganism, Phormidiumtenue var. granuliferum. The Yellowstone conophytons are similar to the Precambrian and the Precambrian Conophytons are astoundingly like those in Yellowstone. The Conophyton–like structures have been induced to form in the laboratory, using pure cultures of this cyanophyte. The results of the work indicate the morphogenetic analysis of at least some fossil stromatolites that can provide physiological data on the constructing microorganisms.