GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz) is a user-friendly web-based tool for exploring plant genomes across including crop plants. GOLEM enables the analysis of diverse plant tissues, encompassing sporophytic organs (e.g., leaves) as well as male gametophytic developmental stages (e.g., antheridia, pollen stages, and sperm cells). The platform allows detailed investigation of the localization and distribution of cis-regulatory elements (CREs) within gene promoters, particularly in regions proximal to the transcription start site (TSS) and translation start codon (ATG). Gene sets can be defined based on tissue-specific expression levels derived from transcriptomic datasets. In addition, genome-wide analyses independent of transcriptional activity facilitate comparative studies of regulatory motif distribution and support investigations into the evolutionary dynamics of CREs across the plant Tree of Life. We demonstrate the utility of GOLEM through analyses of motifs associated with male gametophyte development (e.g., LAT52, MEF2, and DOF_core), hormone-responsive elements (e.g., GCC-box and ARR10_core), and conserved regulatory motifs (e.g., TATA-box, ABRE, TC-element, I-box, and DRE/CRT element). Furthermore, we present a novel update implemented in a private version of GOLEM that enables users to securely analyze their own unpublished datasets.