Segregation, homology and linkage of 33 random amplified polymorphic DNA (RAPD) markers were studied in three trees [P304, E1101 and F1 (cross P315 × E1101)] of Scots pine (Pinus sylvestris L.). Markers were selected on the basis of a RAPD map constructed earlier for F1. Markers from three linkage groups were studied in P304 and E1101. In both P304 and E1101, 14 markers (42%) were heterozygous. Segregation deviating from 1:1 was found for three markers in P304 and one marker in E1101. With the restriction pattern test, two out of the 33 loci studied (6%) were found to be not homologous to the corresponding fragment in F1. Both of these loci were heterozygous, and they were not linked to any markers, which confirmed their nonhomology. Homologous heterozygous markers segregating 1:1 were mostly linked with similar order in P304 and E1101 as in F1. The results suggest that it might be necessary to verify the homology of comigrating fragments before using them even across individuals. It will often be desirable to use other codominant markers together with RAPDs.