Interspaced repetitive DNA elements and segmental duplications have been extensively analyzed in fishes through physical chromosome mapping methods, providing a better comprehension of the structure and organization of the genome of this group. In order to contribute to this scenario, a sequence integration study of different classes of repetitive DNA with high resolution physical chromosome mapping was performed in Sorubim lima. Fluorescence in situ hybridization (FISH) and fiber-FISH with probes for 18S and 5S rRNA genes, TTAGGGn sequence and non-LTR retrotransposon family members Rex1, Rex3 and Rex6 showed that non-LTR elements may be dispersed in the chromosome set with relative concentration in heterochromatic regions, as shown by Rex1, or may even intercalate in 45S rDNA and the telomeric sequence, as found for Rex3 and Rex6. These results reinforce the presence of preferential regions of retroelement accumulation and contribute to a better understanding of the genomic organization of some repetitive DNA classes in fishes.