The green macroalga Ulva prolifera has a number of variants, some of which are asexual (independent from sexual variants). Although it has been harvested for food, the yield is decreasing. To meet market demand, developing elite cultivars is required. The present study investigated the genetic stability of asexual variants, genotype (hsp90 gene sequences) and phenotype variations across a temperature gradient (10–30 °C) in an apomictic population. Asexual variants were collected from six localities in Japan and were isolated as an unialgal strain. The hsp90 gene sequences of six strains were different and each strain included multiple distinct alleles, suggesting that the strains were diploid and heterozygous. The responses of growth and sporulation versus temperature differed among strains. Differences in thermosensitivity among strains could be interpreted as the result of evolution and processes of adaptation to site-specific environmental conditions. Although carbon content did not differ among strains and cultivation temperatures, nitrogen content tended to increase at higher temperatures and there were differences among strains. A wide variety of asexual variants stably reproducing clonally would be advantageous in selecting elite cultivars for long-term cultivation. Using asexual variants as available resources for elite cultivars provides potential support for increasing the productivity of U. prolifera.