This article gives an overview of the biosensors for the analysis of mycotoxins, marine toxins and cyanobacterial toxins, describing in depth the electrochemical biosensors that incorporate nanobiotechnological concepts. Firstly, it presents tailor-designed biomolecules, such as recombinant enzymes, recombinant antibody fragments and aptamers as novel biorecognition elements in biosensors. It also reviews the use of metallic nanoparticles (NPs) and carbon nanotubes (CNTs) aiming at improving the electrochemical transduction strategies. Finally, the exploitation of magnetic particles (MPs) as immobilisation carriers in flow-systems and the development of arrays are also described. The incorporation of these nanobiotechnological concepts provides with electrochemical biosensors with superior analytical performance in terms of specificity, sensitivity, stability and analysis time.