The most numerous limestone caves are in the smallest national park in Poland (the Ojców National Park). A total of 50 algal samples were collected from ten caves, each having different environmental factors such as light intensity, temperature and humidity. The morphological and ecological variability of cyanobacteria and algae were studied using fresh samples, cultures grown on agar plates, and documented with TEM, SEM and LM. Light microscopic observations showed that aerophytic cyanobacteria were the most important component of the cave′s photosynthetic microflora. Among cyanobacteria, the following genera were frequently encountered: Aphanocapsa, Chroococcus, Gloeocapsa, Leptolyngbya, and Synechocystis. Whereas the green algal genera, Apatococcus and Klebsormidium, often occurred with Chlorella, Muriella, Neocystis and the diatoms, Orthoseira and Pinnularia. Most of the algal species appeared to be cosmopolitan, ubiquitous, had simple nutrition requirements and wide ecological tolerance (they reproduced rapidly and were easily adaptable to new conditions). The cave′s microhabitats offered relatively stable microclimatic conditions and they seemed to be responsible for the observed distribution of aerophytic algae and cyanobacteria. The Shannon-Wiener index (H′) ranged between 4.9 and 3.9, and the Kruskal-Wallis test showed that these differences were statistically significant.