This study describes the first report on saxitoxins (STXs) and anatoxin-a (ANTX-a) production by cyanobacteria in Lithuanian lakes. Seasonal fluctuation patterns for neurotoxins were determined in samples collected from eutrophic lakes during July–September. Strains of Aphanizomenon gracile, A. flos-aquae, Cuspidothrix issatschenkoi, Sphaerospermopsis aphanizomenoides and Anabaenopsis cf. elenkinii were also isolated from the lakes and screened for the occurrence of neurotoxic STXs, ANTX-a and for the cytotoxin cylindrospermopsin (CYN). The highest concentration of STX (up to 1.06 µg l^–1 in Lake Jieznas) was detected during July‒August and coincided with a predominance of A. gracile in the phytoplankton. Of the isolated strains, only A. gracile was confirmed to be a producer of STXs by chemical (LC-MS/MS) and genetic (sxtA) methods. Sequencing of the phycocyanin intergenic spacer and flanking regions (cpcBA) revealed that A. gracile formed a genetically homogenous group. Only trace amounts of ANTX-a were detected in field samples (up to 0.31 µg l^–1 in Lake Širvys). CYN was detected in neither the bloom samples nor in the isolated strains.