Both guanine-cytosine content and nucleosome occupancy are higher in exons than in introns. In this study, the association between the frequencies of the dinucleotide sequences and the nucleosome occupancy of the exons and introns of the genes of Aspergillus fumigatus, Aspergillus nidulans, and Aspergillus oryzae was studied. The frequency of the dinucleotide sequences AA (TT), AT, and TA in the introns was more than that in the exons. In addition, the frequency of these sequences in the regions of the exons with low nucleosome occupancy was more than that in the regions with high nucleosome occupancy. On the other hand, the frequency of CC (GG), CG, and GC in the exons and in the regions of the exons with high nucleosome occupancy was higher than that in the introns and in the regions of low nucleosome occupancy, respectively. Interestingly, the frequency of the dinucleotide sequence AC (GT) was similar in the exons and introns of A. fumigatus. In A. nidulans, the frequency of AG (CT) and CA (TG) was similar in the regions of the exons with high and low nucleosome occupancy. In A. oryzae, the frequency of AG (CT) and GA (TC) was similar in the regions of the exons with high and low nucleosome occupancy. This study showed the conserved and varied dinucleotide sequences among the three species of Aspergillus.