This book presents the fundamental issues in phylogeny estimation. Especially for Mathematicians to realize the basic problems of phylogeny inference. In this book we discussed about the circumstances under which any mathematical tool might be suitable or problematic. In this book, the mathematics we used, covered a variety of sub fields like graph theory, combinatorics, probabilities and statistical tools. As is true in other forms of art, success is ultimately determined not by the sophistication of tools and techniques but by how the tools and techniques are put to use. Make the best use of this book and good luck.