Summary: Phylogeny reconstruction is fundamentally crucial for molecular evolutionary studies but remains computationally challenging. Here we present CloudPhylo, a tool built on Spark that is capable of processing large-scale datasets for phylogeny reconstruction. As testified on empirical data, CloudPhylo is well suited for big data analysis, achieving high efficiency and good scalability on phylogenetic tree inference. Availability and Implementation: https://github.com/XingjianXu/cloudphylo Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics online.