The chromosomes of the queen scallop Aequipecten opercularis were studied using conventional Giemsa staining, chromosome measurements, C-banding, silver staining, and fluorescent in situ hybridization (FISH) with 18S-28S rDNA and 5S rDNA probes. The karyotype (2n = 26) consists of large metacentric (pairs 1 and 2), telocentric (pairs 3, 4, 5, 6, 7, 8, and 9), and small metacentric chromosomes (pairs 10, 11, 12, and 13). The C-bands observed can be described as major and minor C-bands which are differentiated according to the intensity of the fluorescence and the frequency of the detection. Major C-bands were found on the long arm of the chromosome pairs 6, 7, 8, and 9 in an intercalary or subterminal position. Minor C-bands were located in the centromeric region in all chromosomes of the complement and also on one arm of pairs 12 and 13 in a terminal position. Silver spots were detected on the telomere of the long arms of one or two chromosomes of pair 7 in every case, although in two individuals up to four additional silver spots were detected. These were located on pairs 8 and 9 in the same position as the C-bands. 18S-28S ribosomal genes were found by FISH on the long arm of chromosome pair 7. 5S ribosomal genes were located subterminally on one arm of metacentric pair 1, but two sites were differentiated in the case of elongated chromosomes. The results obtained allow for the identification of at least six different chromosome pairs in A. opercularis and contribute to the construction of an idiogram that is suitable for gene mapping and establishing accurate interspecific comparisons in scallops.