Cylindrospermopsis raciborskii is a filamentous, potentially toxic, bloom-forming cyanobacterium in tropical and temperate freshwaters. Its high competition and ability of produce toxins have made of this cyanobacterium one of the most studied in the ecological and public health fields. A clonal culture described as C. raciborskii strain D9 (Brazil), produces Paralytic Shellfish Poisoning (PSP) toxins; however, differed from C. raciborskii due to the presence of anomalous heterocysts (N-fixing specialized cells characteristic of the species). C. raciborskii strain CS-505 (Australia) produces cylindrospermopsin (CYN). In spite of these phenotypic differences, strains D9 and CS-505 present 99.7% of identity at the 16S rRNA gene. We have sequenced the complete genome of these toxic strains; the first for cyanobacteria producing either PSP- or CYN-toxins. The genome sizes, the smallest found for filamentous cyanobacteria, are 3.3 and 3.9 Mbp for D9 and CS-505, respectively, fairly different for so closely related organisms. The genome comparison revealed a large amount of transposition elements and repeated sequences, as well as secondary metabolite pathways in CS-505 genome, demonstrating a high plasticity and signatures of large genome species. In contrast, strain D9 presents a high number of genes involved in DNA modification (protection) and repair and lacks all the nitrogen fixation genes. In summary, it seems the strain D9 have undergone genome reduction and implies a resistance of strain D9 to the acquisition of new functions and also raise the possibility of a misclassification of this strain.