Cyanobacteria are a rich source of biologically active compounds used in pharmacology and biotechnology. Due to their high capacity of adaptation, which is reflected in the production of diverse metabolites, including toxins, these microorganisms are able to inhabit very different environments. In this work, water and ethanol extracts from 11 cyanobacterial strains derived from the Baltic Sea (Microcystis, Synechocystis, Leptolyngbya, Pseudanabaena, Lyngbya, Phormidium, Nodularia and Anabaena genera) were screened for anticancer activity. MCF-7 human breast cancer and HeLa cervical cancer cell lines, as well as HDFa normal human fibroblasts, were used. Three extracts derived from Pseudanabaena sp., Pseudanabaena cf. galeata and Microcystis aeruginosa revealed potent and selective antiproliferative activities against cancer cells. The mechanism of the anticancer activity was explored in MCF-7 cells, and was found to rely on the inhibition of the pro-survival Akt kinase and induction of cell death. The peptide profiles of selected cyanobacterial extracts were determined using LC-MS/MS, and classes of bioactive compounds that might be potentially responsible for the observed anticancer activities are presented.