There exists a strong need for a qualitative spatial knowl-edge representation that is capable of modeling and of rea-soning about knowledge of genomic structures. The reason-ing component can help to improve the biological plausibil-ity of existing alignment approaches for bacterial genomic DNA sequences, which at present relies exclusively on similarity comparisons on the string level. Genomic DNA sequences of bacteria, even within the same species, can be highly variable. This variability exists not only at the string level, but also at the structural level, i.e. the order of genes and their coding is less conserved as could be expected. Therefore, the comparisons of genomic DNA sequences should not only use the sequence similarity on the string level, but they should rather be extended to the structural level. We present a concept to support the alignment proce-dure with one-dimensional spatial knowledge of genomic structures like genes and their regulatory regions, which is expressive since it allows a specification and reasoning about spatial relations between genomic structures by dis-junctions of qualitative relations.