A useful approach to rapid identification of Chlorella strains in a single cell of Paramecium bursaria was developed. A “nested” PCR-based method with primers flanking intron insertion sites in the 18S rRNA gene of Chlorella ensured fast screening of large P. bursaria collections for the presence of the two basic types of Chlorella endosymbionts without isolating them in pure culture. The method applied to several Paramecium isolates showed that the P. bursaria clone T-24-5 from Tajikistan presumably bears an atypical Chlorella symbiont possessing an atypical intron in the 18S rRNA gene. This sequence was cloned and sequenced. BLAST analyses of the intron sequence cloned showed the presence of 136-bp stretch highly similar to the Chlorella virus intron fragment in major capsid protein Vp54 gene. The similarity value indicated a common origin of the sequences and suggested that the horizontal transfer of this DNA fragment had happened between the chlorella and the virus attacking it.