Eukaryotic genomes evolve through accumulation of small-scale changes like point mutations, nucleotide insertions and deletions in their sequences. On the other hand, chromosomal rearrangements (inversions, translocations, fusions and fissions) can also contribute to reshuffling of the gene order. It is widely assumed that there is correlation between nucleotide and structural evolution. However, counterexamples coming from comparative sequence analyses were also revealed. As each genome has their own uniqueness, further investigation of genome evolution can help us to better understand how the different genomes were organized and changed, when and why natural selection acted. The fission yeasts (Schizosaccharomyces) form an ancient clade within the Ascomycete fungi and have a distinct life history from other yeasts. It has been reported that conservation of the gene content within Schizosaccharomyces is significantly higher than that within Saccharomyces or Kluyveromyces. Moreover, gene order and gene structure of the fission yeasts are also more conserved than expected from levels of their amino acid divergences. These observations suggest that fission yeast amino acid sequences evolve anomalously fast or that their genome structures are unusually stable. Thus, stable genome structures of fission yeasts could be consequences of insufficient rearrangements, and because of this the perceived genome conservation is just a remnant of the ancestral gene order. According to another scenario, genetic rearrangements could occur frequently, but the ancient gene order still was maintained by natural selection. In order to gain more information on the topic of genome evolution of the fission yeasts, a comparative study of sequences was carried out. Sequences of 30 fungal species of several different clades were compared and sequence evolution and genome rearrangements were investigated. We created global and genus level phylogenetic trees using the concatenated sequences of 18 putative orthologues. In addition to that, we performed whole genome alignments among the species and estimated the minimum number of rearrangements occurred by the help of locally collinear blocks found (chromosomal fragments, which does not contain any rearrangements). Thereafter, we compared the branch lengths of the phylogenetic trees to the number of rearrangements. Our results suggest that it was not only amino acid sequences of the fission yeasts that were evolving fast but their genomes were also undergoing numerous rearrangements. That is, observed conservation of the gene content and gene order within the fission yeasts probably does not come from incomplete genome reshuffling. We assume that stable genome structures of the Schizosaccharomyces species are likely to have been maintained by natural selection rather than as a result of the fact that there had been few chromosomal rearrangements during their evolution. Spliceosomal introns can occupy nearby rather than identical positions in orthologous genes (intron sliding or -shifting). S...