The chapter revisits the concept of homology with respect to the whole genes as well as a site in a gene. Gene homology due to speciation (orthology) vs. gene duplication (paralogy) are contrasted, with emphasis on why orthologs are crucial for reconstructing species relationships. The challenges posed by nuclear mitochondrial pseudogenes (numts) are explained, highlighting their misleading phylogenetic signals. Broader issues of gene duplication followed by gene deletion resulting in hidden paralogy are discussed. Homology vs. homoplasy at the level of a site in a gene is explored with examples. Convergence, parallel evolution and reversal are introduced as the potential sources of homoplasy. Through case examples, the chapter underscores the importance of critically evaluating sequence datasets for true homology before analysis.