In this paper, a novel and facile electrochemical sensor for the simultaneous detection of adenine and guanine was fabricated based on 3,4,9,10-perylene tetracarboxylic acid noncovalently modified multiwalled carbon nanotubes. It exhibited good electrochemical responses toward the oxidation of adenine and guanine with a linear ranges covering 1.74 x 10(-7) -2.09 x 10(-5) M and 7.59 x 10(-8) -2.09 x 10(-5) M, and the corresponding detection limit of 5.81 x 10(-8) M and 2.53 x 10(-8) M (S/N = 3), respectively. Moreover, the fabricated sensor was employed for the exploration the possible electrochemical reaction mechanism of guanine supported by cyclic voltammetry experiments (CV). Eventually, the proposed sensor was applied in the determination of adenine and guanine contents in calf thymus DNA with satisfactory results, which has the great potential application in the sensitive monitoring of electroactive bio-molecules.