In this study; the synthesis, structural characterization and electrochemical sensor properties of SWCNTs covalently functionalized with different BODIPY derivatives toward guanine and adenine were investigated. The target SWCNTs-BODIPY hybrids (CB, CB1 and CB2) were synthesized by the reaction of azido functionalized SWCNT with the BODIPY derivatives containing terminal ethynyl group via the Click reaction. Structural characterization of SWCNT-BODIPY hybrid materials was performed by Raman, UV–visible, FTIR spectroscopies and thermogravimetric analysis. The surface morphologies of the new hybrids were evaluated by SEM and TEM. The sensing behavior of these hybrid materials was investigated to detect guanine and adenine in PBS. CB1 hybrid material showed the better sensor properties with the detection limits of 1.07 μM and 2.91 μM for guanine (G) and adenine (A), respectively. The quantification limits were found to be 3.21 μM for guanine and 18.6 μM for adenine in PBS. The applicability of the modified electrode for the detection of G and A in DNA from calf thymus was demonstrated with the standard addition method.