Arctic char (Salvelinus alpinus) and brook trout (Salvelinus fontinalis) hybridize and their offspring is viable and fertile. This may be a real treat for the native European stocks of Arctic char which gene pools might be unintendedly contaminated with the genetic elements of brook trout. On the other hand, hybrids of these two species are appreciated by customers and have some potential for the aquaculture. Moreover, Salvelinus hybrids and backcross individuals are interesting models in the research focused on influence of hybridization on the genomic organization and chromosome rearrangements. Thus, the main goal of the present study was to examine chromosomes of Arctic char × brook trout F1, F2 hybrids and backcross individuals and compare with genomic information concerning parental species to recognize karyotypic changes provoked by the hybridization events. Application of conventional and molecular (FISH) techniques allow to identify characteristic chromosomes for both parental species in the hybrid progeny and show multiplicity of cytotypes among different types of crosses with variability in structure and number of chromosome (81-85) and chromosome arm (99-101). Chromosome fragment was detected in the karyotype of one F1 and one backcross individual and the presence of one triploid (3n) fish was documented. Occurrence of chromosomes containing internally located telomeric sequences (ITS) inherited after brook trout or both parental species was shown in F1 and backcross progeny. Moreover, additional CMA3-positive signal on chromosome from Arctic char pair no. 2 in F1 fish and interstitially located active NOR visible on subtelo-acrocentric (F2 hybrid) and acrocentric (Sf × H individual) chromosomes were detected. Described polymorphic chromosomes together with specific, interstitial location of CMA3-positive found in F2 and Sf × H hybrids and DAPI-positive regions observed in H × Sa fish at different uniarmed chromosomes pair presumably are remnants of chromosomal rearrangements. Provided results strongly indicate that the hybridization process influenced the genome organization in the Salvelinus hybrid progeny.