The phylosamp R package provides tools for conducting and evaluating sample size calculations using pathogen genomic data in phylogenetic studies. It supports three common epidemiological scenarios: determining whether infections are linked through transmission (linkage scenario), estimating the prevalence of a specific pathogen lineage or variant of concern (variant tracking scenario), and assessing whether transmissibility differs between groups of infected hosts (relative R scenario). By tailoring sample size estimates to these specific contexts, the package helps researchers design efficient genomic studies that are appropriately powered to answer key public health questions.