Genome size (the C-value) is known to vary considerably among organisms, but is relatively constant among individuals of the same species. To determine the genome size in the Northern Chilean scallop Argopecten purpuratus, two populations were analyzed by measuring the fluorescence signal in hemocyte nuclei stained with DAPI. The fluorescence intensity was measured during a fluorescence-fading period by image analysis (fluorescence fading method). The area under the curve during a fading period was associated with the genome size, thus we determined the C-value in the Arica population as 1.057 ± 0.057 pg of DNA and 1.139 ± 0.066 pg of DNA for the Tongoy population. The interindividual variation was smaller that 6% for both populations. Variance analysis was performed to detect the effects of organisms and population in the genome size of A. purpuratus. Significant differences were detected between Arica and Tongoy populations (P = 0.0011). The genome size of Tongoy population was larger statistically compared with the Arica population. Several hypotheses are discussed about genome size variation.