Members of the family Geminiviridae have single-stranded (ss), circular DNA genomes that are encapsidated into non-enveloped quasi-icosahedral twinned (geminate) particles, causing yield losses in several economically important crops worldwide. Sequence-based approaches used for molecular characterization of Geminiviridae genomes, associated with powerful bioinformatic tools, provided a better picture about the true extent of the Geminiviridae species diversity. This chapter describes procedures to reconstruct Geminiviridae phylogenetic relationships based on coat protein (CP) and replication-associated protein (Rep) amino acid sequences and full-length nucleotide genomes using both maximum likelihood (ML) and Bayesian inference (BI) approaches. Although topological incongruences can be observed among the ML phylogenetic trees for CP, Rep, and genome sequences, suggesting inter-genera recombination, Geminiviridae exemplar viruses predominantly cluster according to the genera recognized by the International Committee on Taxonomy of Viruses.