A major thrust in the laboratory of Louise Lewis is diversity and systematics of green algae (Phylum Chlorophyta) living in the soils of North American deserts. These unicellular green algae are capable of tolerating the harsh conditions posed by desert soil environments, and represent an important (yet not well understood) component of desert microbiotic crust communities. The 18S rDNA sequences of a number of green algal isolates have been determined, and these data suggest that several lineages of green algae have diversified within deserts. One might be tempted to think that the green algal cells isolated from desert soils are simply the result of spores dispersed into deserts from distant aquatic sources. This study shows that the 18S sequences of these desert isolates are more divergent from their nearest aquatic relatives than would be predicted if they were merely incidental visitors. We characterize the molecular phylodiversity of desert green algae and demonstrate with a Bayesian analysis of 150 green algal 18S sequences that all freshwater classes of green algae have yielded desert lineages. The numerous transitions from desert to aquatic existence apparent from the phylogeny argue that it is no longer accurate to portray land plants as resulting from a single origin. The highly celebrated origin leading to the embryophytes is but one of many transitions to terrestriality.