Algal microremains were encountered during palynological investigation of deposits filling two Miocene palaeosinkholes excavated in the Tarnów Opolski and Górażdże quarries. Algal microfossils of 40 species were identified, most of which are frequent non-pollen palynomorphs occurring in Neogene deposits. The microfossils most frequently found in all studied samples belong to the genera Sigmopollis and Botryococcus. Both algal assemblages contain a significant proportion of resting cells (zygospores = hypnozygotes) such as Cycloovoidites, Diagonalites, Megatetrapidites, Ovoidites, Stigmozygodites, and Tetrapidites, probably fossil zygospores of members of the Zygnemataceae family (Mougeotia, Spirogyra, Zygnema). Some specimens probably related to desmid zygospores (Closteritetrapidites, Monopunctites, Planctonites), freshwater dinoflagellate cysts, and Prasinophyceae (Leiosphaeridia) were found. Most of the identified fossilised remains of algae are often seen in sediments indicating meso- to eutrophic conditions and are characteristic for stagnant or slowly flowing shallow waters. Fossil algae of Pediastrum and Tetraedron genera were recorded in samples from the Górażdże palaeosinkhole, suggesting small differences in the aquatic habitat (e.g. water depth) between ponds in the sinkholes. Three new fossil species related to zygospores of the Zygnemataceae are described: Ovoidites vangeelii sp. nov., Tetrapidites grandis sp. nov., and Tetrapidites opolensis sp. nov.