Microcystins are cyanobacterial toxins, effectively inhibiting protein phosphatases 1 and 2A, enzymes that are involved in plant cytoskeleton (i.e. microtubules and F-actin) organization and cell cycle progression. Therefore, studies on the toxicity of cyanobacterial products on plant cytoskeleton have so far focused mainly on the effects of microcystin variants on microtubules. In this study, we investigated the effects of the extracts of two non-microcystin-producing (NMP) cyanobacterial strains, Microcystis viridis TAU-MAC 1810 and Planktothrix agardhii TAU-MAC 0514, on the cytoskeleton and cell cycle of Oryza sativa (rice) root cells. Rice seedling roots were exposed for various time periods (1, 12 and 24h) to aqueous extracts of the aforementioned strains. Treated root tips were excised, fixed and underwent either immunostaining for α-tubulin or fluorescent phalloidin staining for F-actin, and DAPI staining for DNA. Fluorescent specimens were observed by confocal laser scanning microscopy (CLSM). Corrected total cell fluorescence (CTCF) was calculated to quantify cytoskeletal disorders. Cell cycle stages were recognized according to cytoskeletal arrangement and/or chromatin state, in order to assess cell cycle progression alterations, and the data were statistically analyzed. Also, a number of treated seedlings were stained with Evans Blue to determine dead cells. Treatment with the extracts affected both microtubules and F-actin, while cell cycle stage frequency was also altered. Although belonging to well-known toxic, microcystin-producing species, the above cyanobacterial strains have been found (by LC-MS/MS analysis) not to produce microcystins. These findings suggest that bioactive cyanobacterial compounds, other than microcystins, could be able to disrupt the cytoskeleton and cell cycle progression in plant cells.