In all 29 polycystine radiolarian species were obtained from surface seawater on May 28, 1999, using a plankton-net at one station (Site 990528; 26°37′18″N, 127°47′35″E) approximately 5 km northwest of Okinawa Island, Japan. In most polycystine radiolarians of the orders Nassellarida and Spumellarida symbiotic algae were observed under light microscopy. The light microscopic (LM) images of the symbionts, however, varied in clarity among individuals because of the variations in microanatomy of the host radiolarian cells. On the other hand, epifluorescence microscopic (EFM) observation easily detected and confirmed the existence of the algal symbionts within the host cytoplasm even in radiolarians such as Dictyocoryne truncatum (Ehrenberg) that include algal symbionts in the depth of the cytoplasm. The chloroplasts of the algal symbionts emitted autofluorescence in ultraviolet irradiation and they appeared red. That is, the autofluorescence images of the chloroplasts can be used to recognize the existence of the algal symbionts within the host radiolarians. Moreover, staining of the symbiont cells with 4′,6-diamido-2-phenylindle permitted visualization of the nucleus in the center of the symbiont cell, confirming the existence of living endosymbiotic algae within the polycystine radiolarians. Both the LM and EFM observations of eight polycystine radiolarian species revealed the specific patterns of various host-symbiont associations. (1) The investigated polycystine radiolarians all possess algal symbionts, except for one species, i.e. Dictyocoryne profunda Ehrenberg. (2) The size of the algal symbionts depends on the radiolarian species. The symbionts are largely classified into two types based on the size of their diameters, i.e. about 8–10 μm for the larger group and about 5 μm for the smaller one. (3) The algal symbionts show a variety of locations within the host radiolarian cytoplasm. The types of distribution of algal symbionts may be a useful characteristic for radiolarian taxonomy.