A method of determining the base sequence of a nucleic acid by detecting a single dye molecule, which involves the following steps: (1) fixing to a solid surface a nucleic acid molecule or a primer having a sequence complementary to a part of the sequence thereof; (2) annealing the above nucleic acid molecule or primer with the corresponding primer or nucleic acid molecule; (3) supplying a solution containing DNA polymerase and a dye-labeled dNTP or RNA polymerase and a dye-labeled NTP to the fixed nucleic acid molecule and reacting the nucleotide with the 3'-end of the primer to thereby allowing the polymerase to incorporate the nucleotide forming a base pair with the base opposite to the reaction site; (4) detecting the dye-labeled dNTP or NTP thus bonded; (5) disrupting the dye molecule of the bonded dye-labeled dNTP or NTP; (6) repeating the procedures of the steps (3) to (5) while successively changing the type of the dye-labeled dNTP or NTP so as to bond the dNTP or NTP forming a base pair with the nucleotide of the nucleic acid molecule; and (7) determining the base sequence of the nucleic acid molecule based on the dNTP or NTP thus bonded.