Cyanobacterial blooms are frequent in the North-Eastern region of Slovenia, where the agricultural activities are intensive, resulting in higher water eutrophication. In a two year monitoring program we identified eighteen blooms of cyanobacteria, fifteen being hepatotoxic by intraperitoneal mouse bioassay. The approximate LD 100 varied from 50-1000 mg/kg (dry cell weight/animal weight) and gross pathological signs were characteristic of cyanobacterial hepatotoxins. Frequently the blooms were dominated by the most common and cosmopolitan species Microcystis aeruginosa. Other bloom forming species were M. wesenbergii, Oscillatoria rubescens, Anabaena flos-aquae, and Aphanizomenon flos-aquae. Using high-performance liquid chromatography (HPLC), three hepatotoxins were identified, microcystin RR being the most frequent and present in highest amounts, LR, and YR. The phytoplankton analysis revealed that several different species of cyanobacteria were present in the water bodies at the time of the blooms. Although present in various water bodies, filamentous bloom-forming cyanobacteria had no chance to proliferate in the presence of the colonial genus Microcystis. In individual cases we were faced with a bloom in the bloom, meaning that various Microcystis aeruginosa blooms were heavily contaminated with another cyanobacteria, Phormidium mucicola which infested the mucilage of the chroococcal species.