Ciliates, including Paramecium bursaria, possess cell organelles called trichocysts that have defensive functions. Paramecium bursaria is capable of symbiosis with Chlorella sp., and the symbiotic algae are in close proximity to the trichocysts. To clarify the relationship between trichocysts in P. bursaria and the presence or absence of the intracellular symbiotic Chlorella sp., this study compared the regeneration capacity of trichocysts in alga-free and algae-bearing P. bursaria. In addition, trichocyst protein abundance was measured when alga-free P. bursaria specimens were artificially infected with Chlorella sp. After completely removing trichocysts from P. bursaria cells by treatment with lysozyme and observing them after 24 h, the percentage of regenerating trichocysts in the entire cell was significantly higher in alga-free cells than that in algae-bearing cells. There was a significant difference in the trichocyst protein abundance of P. bursaria before and one week after mixing with Chlorella sp. (i.e., after the establishment of symbiosis with the algae). We also developed a simple method for the isolation of high-purity trichocysts to quantify trichocyst protein amounts. This study shows the importance of trichocysts in alga-free P. bursaria as well as their competition with symbiotic Chlorella sp. for attachment sites during the algal infection process.