A new method of genomic maps analysis based on formal logic is described. The purpose of the method is to 1) use mitochondrial genomic organisation of current taxa as datasets 2) calculate mutational steps between all mitochondrial gene arrangements and 3) reconstruct phylogenetic relationships according to these calculated mutational steps within a dendrogram under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as very robust results. Moreover, the method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes (ancestors) of the trees. We started by testing the method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the mutational network of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene rearrangements in deuterostomes and should be applied to many other bilaterian clades.