Ligation is accomplished by a small set of SUMO E3 ligases, with the SAP-MIZ domain-containing (SIZ)-1 and METHYL METHANESULFONATE-SENSITIVE (MMS)-21 ligases having critical roles in stress protection and DNA endoreduplication, respectively. To help identify their corresponding Arabidopsis targets, we combined siz1 and mms21 mutants with proteomic analyses of SUMOylated proteins enriched using an engineered 6His-SUMO1. Through multiple datasets from seedlings grown at normal temperatures or exposed to heat stress, we identified over 1,000 SUMO targets, most of which are nuclear localized. Whereas no targets could be assigned to MMS21, suggesting that it modifies only one or a few low abundance proteins, numerous targets could be assigned to SIZ1, including major transcription factors, co-activators/repressors, and chromatin modifiers connected to abiotic and biotic stress defense, some of which associate into multi-subunit regulatory complexes.