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The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of <i>Echinococcus multilocularis</i> in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (<i>nad2</i>), cytochrome b (<i>cob</i>), and cytochrome c oxidase subunit 1 (<i>cox1</i>), are analyzed. The sequences are represented by sets of material points in a 4D space, i.e., 4D-dynamic graphs. As a visualization of the sequences, projections of the graphs into 3D space are shown. The differences between 3D graphs corresponding to European, Asian, and American haplotypes are small. Numerical characteristics (<i>sequence descriptors</i>) applied in the studies can recognize the differences. The concept of creating descriptors of 4D-dynamic graphs has been borrowed from classical dynamics; these are coordinates of the centers or mass and moments of inertia of 4D-dynamic graphs. Based on these descriptors, classification maps are constructed. The concentrations of points in the maps indicate one Polish haplotype (EmPL9) of Asian origin.