Abstract Summary Current approaches detect conserved genomic order either at chromosomal (macrosynteny) or at subchromosomal scales (microsynteny). The latter generally requires collinearity and hard thresholds on syntenic region size, thus excluding a major proportion of syntenies with recent expansions or minor rearrangements. ‘SYNPHONI’ bridges the gap between micro- and macrosynteny detection, providing detailed information on both synteny conservation and transformation throughout the evolutionary history of animal genomes. Availability and implementation Source code is freely available at https://github.com/nsmro/SYNPHONI, implemented in Python 3.9. Supplementary information Supplementary data are available at Bioinformatics online.