Many freshwater protists harbor unicellular green algae within their cells, but little is known of their degree of integration and specificity. Using algae-targeted PCR of whole ciliate cells collected at irregular intervals over 15 months from Lake Biwa, Japan, we explored the SSU-ITS rDNA of the endosymbiotic algae and its changes over time, obtaining sequences of algal rDNA fragments from four ciliate species. A high proportion of clonal algae was evident within the ciliate cells. The differences observed in those sequences from the SSU through to the ITS region were less than 1%. The name ‘Chlorb’ is proposed for these algae, with the implication that they represent a single ‘species.’ The sequences of the algal DNA fragments were identical for any given host species throughout the collection period, thus we conclude that these four ciliates stably retain their algae over long term. In contrast, algal DNA fragments obtained from Didinium sp. were variable within each sample, which indicates that this ciliate only temporarily holds its algal cells. The ITS1 sequences of Chlorb populations are close (at intraspecific level) to those of algae isolated from ciliates in Austria, which raises the possibility that Chlorb algae are universally shared as symbionts among various ciliates.