Speciation problems are reviewed in the context of biogeography of fresh-water algae. Currently accepted species concept in phycology is based on morphological characters, and according to this concept, most freshwater algal species are considered cosmopolitan. This implies whether they have a highly efficient means of dispersal or their morphological characters are very static through a long evolutionary time. Recent studies of reproductive isolation show that some biological species of fresh-water algae are not so static or may not have such a high power of dispersal means, though some are indeed very static in morphological characters. The life cycle of most freshwater algae is composed of a vegetative cycle of growth and reproduction and a sexual cycle of gametic fusion and meiosis in the zygote, which forms a dormant spore-like structure. Since any freshwater habitat is ephemeral in terms of evolutionary time scale, each species has a capacity of forming germlings from a dormant cell in order to recycle its life history. The genome of freshwater algae, therefore, contains various coadapted gene systems, at least two, for the vegetative and for the sexual cycle. Homothallism and heterothallism are two contrasting mating systems that represent two opposing ways of life to harmonize antagonism between the vegetative stage of growth and reproduction and the sexual and dormant stage. Geographic and ecological distribution, polyploidy, and sex determination are discussed in conjunction with sexual and postzygotic isolating mechanisms.