Specimens of Crassostrea angulata collected from several natural populations, with or without metal contamination, located along the Southwestern coast of Spain were cytogenetically analyzed. The diploid number was 20 and all 10 chromosome pairs were metacentric. The nucleolar organizing regions (NORs) were identified on the telomeric region of the chromosome pair 10 by several methods, including silver nitrate staining (AgNO3), chromomycin A3 staining (CMA3) and fluorescence in situ hybridization (FISH). One or two primary Ag-NORs in the metaphase cells were most frequently found. Very infrequently, one or two secondary NORs were seen. High Ag-NOR and rDNA polymorphisms in both the size and/or the number occurred intra-individually, inter-individually and inter-populationally. However some population-specific Ag-NOR polymorphisms were found to reach or be approaching to a level of significant difference. A comparison of number and frequencies between FISH-rDNA signals and Ag-NORs showed that some NORs were not transcriptionally active. Moreover, presence of pollutants on the medium could be favoring the presence of two NORs per cell more than acting modifying expression on the NORs.