This textbook covers the fundamentals of molecular phylogenetics. Over the past few decades, there has been an exponential increase in DNA sequence data available in public databases, along with the sequencing of complete genomes for numerous organisms. Concurrently, advances in sequence analysis methods and the computational power of computers have significantly progressed. This book consolidates and presents essential information on phylogenetics, detailing various approaches to constructing evolutionary trees, molecular markers, and statistical tests, along with their applications. It also delves into the theoretical foundations of phylogenetic methods, offering a clear overview without overwhelming mathematical details. This approach empowers students to analyze and interpret data accurately and address potential issues in the process. This textbook is designed for students and researchers in taxonomy, biogeography, and evolutionary biology.