The urkingdoms and major divisions of prokaryotes are enormously diverse in their metabolic capabilities and membrane architectures. These ancient differences likely have a strong influence on the kinds of ecological adaptations that may evolve today. Some ecological transitions have been identified as having occurred primarily in the distant past, including transitions between saline and non-saline habitats. At the microevolutionary level, the likely existence of a billion prokaryotic species challenges microbiologists to determine what might promote rapid speciation in prokaryotes, and to identify the ecological dimensions upon which new species diverge and by which they may coexist. Rapid speciation in prokaryotes is fostered by several unique properties of prokaryotic genetic exchange, including their propensity to acquire novel gene loci by horizontal genetic transfer, as well as the rarity of their genetic exchange, which allows speciation by ecological divergence alone, without a requirement for sexual isolation. The ecological dimensions of prokaryotic speciation may be identified by comparing the ecology of the most newly divergent, ecologically distinct populations (ecotypes). This program is challenged by our ignorance of the physiological and ecological features most likely responsible for adaptive divergence between closely related ecotypes in any given clade. This effort will require development of universal approaches to hypothesize demarcations of ecotypes, and to confirm and characterize their ecological distinctness, without prior knowledge of a given clade's ecology.