The electrochemical monitoring of (i) label-free and (ii) indicator based DNA hybridization related to Microcystis spp. (MYC) DNA was explored in this study via multiwalled carbon nanotube (MWCNT) based screen printed graphite electrodes (SPEs). The effect of CNT modification onto SPE was firstly investigated by measuring the oxidation signals of guanine and adenine before/after DNA immobilization onto the surfaces of bare SPE, MWCNT-SPE and SWCNT-SPE in combination with differential pulse voltammetry. MYC-DNA hybridization was monitored by following two procedures and measuring the guanine oxidation signal and the reduction signal of cobalt-phenanthroline Co(phen)33+. Voltammetric results were complemented with electrochemical impedance spectroscopy (EIS).