Two distinct marker chromosomes, presenting with intercalated C- and distamycin A-Dapi-positive regions, were observed in a metastatic and a primary melanoma. To establish the origin of these heterochromatic sequences, we performed in situ hybridization analysis using specific probes for human repetitive DNA. The marker of the primary melanoma, m2, a der 16 chromosome resulting from the translocation of the 1q12-qter segment to band q23 of chromosome 16, showed specific hybridization with Sau3A but not with EcoRI sequences at the interstitial C-band. Thus the origin of this region from the normal chromosome 1 pericentromeric heterochromatin, containing both EcoRI and Sau3A sequences, could be established. On the other hand, the marker of the metastatic melanoma, m1, a der 1 chromosome showing an abnormally banded region inserted between 1q11 and 1q21-qter, failed to give any hybridization signals at the C- and distamycin A-Dapi-positive band when the same EcoRI and Sau3A probes were used. Furthermore, no hybridization was observed using either a probe for SatIII-specific sequences (QP23), mapping to chromosome 9 heterochromatic block, or LS6BB, a ribosomal DNA probe. From these data we speculate that more complex molecular rearrangements may have occurred during the transposition of heterochromatin from its original site to m1. The heterochromatin change found in m1 may be related to advanced stages of malignancy.