Abstract Response to elevated Zn concentrations of two various ecotypes of the periphytic green alga Stigeoclonium tenue Kütz. was studied. An ecotype, classified as S. tenue (T), isolated from ditches containing mining water, was Zn-tolerant. It was able to grow and reproduce by zoospores at external Zn concentrations ≥15 μM. Another ecotype of this species, classified as S. tenue (S), isolated from unpolluted lake water was Zn-sensitive; its exposure to 15 μM and higher Zn concentration caused a significant decrease of chlorophyll content, inhibition of zoospore settling and, finally, death. The morphology of mature thalli of these two ecotypes cultivated under the same conditions also differed, i.e. the erect system of S. tenue (T) consisted of filaments with long, narrow cells, while the erect system of S. tenue (S) consisted of filaments with shorter, barrel-shaped cells. Therefore, S. tenue (S) thalli were more compact than thalli of S. tenue (T). S. tenue (T) exposed to 30 μM Zn for 3 weeks was able to release zoospores, while S. tenue (S) was not. The two algal ecotypes differed in the amount of intracellularly accumulated Zn and Pb. The Zn-tolerant ecotype S. tenue (T) accumulated (independently of the exposure conditions like pH and orthophosphate concentration) significantly more Zn and Pb than the Zn-sensitive ecotype. A new cytochemical method was developed to visualise intracellular Zn in algal cells. In the long-term, Zn-exposed cells of both ecotypes, pink-orange Zn–dithizone complexes were observed in peripheral vacuoles, while in cells not exposed to Zn, no deposits were present. The data obtained suggest that the Zn-tolerant ecotype S. tenue (T) is able to detoxify the excess of accumulated zinc more effectively than the sensitive ecotype, however, vacuolar Zn compartmentalisation does not seem be the main tolerance mechanism.