Abstract Phylogenomics data have grown exponentially over the last decades. It is currently common for genome-wide projects to generate hundreds or even thousands of phylogenetic trees and multiple sequence alignments, which may also be very large in size. However, the analysis and interpretation of such data still depends on custom bioinformatic and visualisation workflows that are largely unattainable for non-expert users. Here, we present PhyloCloud, an online platform aimed at hosting, indexing and exploring large phylogenetic tree collections, providing also seamless access to common analyses and operations, such as node annotation, searching, topology editing, automatic tree rooting, orthology detection and more. In addition, PhyloCloud provides quick access to tools that allow users to build their own phylogenies using fast predefined workflows, graphically compare tree topologies, or query taxonomic databases such as NBCI or GTDB. Finally, PhyloCloud offers a novel tree visualisation system based on ETE Toolkit v4.0, which can be used to explore very large trees and enhance them with custom annotations and multiple sequence alignments. The platform allows for sharing tree collections and specific tree views via private links, or make them fully public, serving also as a repository of phylogenomic data. PhyloCloud is available at https://phylocloud.cgmlab.org