Allelic silencing is an important mechanism to cope with gene dosage changes in polyploidy organisms that is well known in allopolyploid plants. Only recently, it was shown in the allotriploid fish Squalius alburnoides that this process also occurs in vertebrates. However, it is still unknown if this silencing mechanism is common to other allopolyploid fish; and which mechanisms might be responsible for allelic silencing (AS). We addressed these questions in a comparative study between Squalius alburnoides and another allopolyploid complex, the Amazon molly (Poecilia formosa). We examined the allelic expression patterns for three target genes in four somatic tissues of natural allo-anorthoploids and laboratory produced tri-genomic hybrids of S. alburnoides and P. formosa. Also, for both complexes, we evaluated the correlation between total DNA methylation level and the ploidy status and genomic composition of the individuals. We found that AS also occurs in other allopolyploid organisms besides the single one that was previously known. We found and discuss disparities within and between the two considered complexes concerning the pattern of allele specific expression and DNA methylation levels. Disparities might be due to intrinsic characteristics of each genome involved in the hybridization process. Our findings also support that long-term evolutionary processes have an effect onto the allele expression patterns and possibly also on DNA methylation levels.