Supplementary Dataset to the manuscript "Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multi-drug resistant lineages", by Lucy F. Grist, Alice Brown, Noel Fitzpatrick, Giuseppina Mariano, Roberto M. La Ragione, Arnoud H. M. van Vliet and Jai W. Mehat. The dataset contains 2,276 genome assemblies of Staphylococcus pseudintermedius, combining three different types of data, made available here for open research purposes: Genome assemblies of 110 new UK isolates not previously available. These have also been uploaded into NCBI genome, and have a SCpseud_UoSXXX filename and the SRR code for NCBI SRA. Genome assemblies (1,144) obtained from the NCBI Genome repository, recognisable by the StaphpseudXXXX_GCA filenames Genome assemblies (1,022) generated from sequencing reads obtained from NCBI SRA and the ENA repositories, recognisable by the StaphpseudXXXX_SRR and StaphpseudXXXX_ERR filenames. Genomes were assembled using Shovill version 1.1.0 (https://github.com/tseemann/shovill) using the default settings and the Spades assembler. Only genomes with N50>50 kb, L50<20, and a number of contigs <200 were included in this study.