From a phylogenetic perspective, most plant biodiversity lie in the algae, which comprise nine divisions distinct in cell architecture. In the past decade or so, molecular phylogenies have revealed that many algal divisions are only distantly related, and belong to five different supergroups of eukaryotes. The scattered and distant distributions of algae are interpreted as the result of separate endosymbioses that occurred in various lineages of eukaryotes. Endosymbiosis is a major driving force of algal evolution and diversification, and therefore, is a key process in understanding plant evolution. In this paper, the process of plastid acquisition via endosymbiosis is considered, focusing on the evolution of protein transport machinery, which is indispensable for establishing new lineages of algae, and simultaneous lateral gene transfer from the symbiont to the host nucleus. The current understanding of protein transport diversity is reviewed in relation to the membrane topologies of plastids. The endosymbioses found in various algae and protists are natural occurrences in plant evolution and diversification, and exhibit intermediate stages of plastid acquisition. The conditions necessary for plastid establishment are also considered, using several examples of ongoing endosymbioses.