The study of evolutionary relationships is an important endeavor in the field of Bioinformatics. The fuzzification of genomes led to the introduction of a “fuzzy polynucleotide space”, which has been successfully used in classification and clustering of amino acids, thereby suggesting a possible application in phylogeny. As phylogenetic trees illustrate similarities and evolutionary relationships among different taxa, through this study we attempt to determine the efficacy of the fuzzy polynucleotide space in phylogenetic tree reconstruction, and discuss its implications in evolutionary biology.