<span class="paragraphSection"><div class="boxTitle">Abstract</div>Histone demethylases serve essential functions in plant growth and development across various species. However, their roles in <span style="font-style: italic;">Glycine max</span> remain largely unexplored. This study identified <span style="font-style: italic;">GmJMJ19</span> and <span style="font-style: italic;">GmJMJ20</span>, encoding JmjC domain-containing proteins. They exhibit circadian rhythmic expression patterns and interact with LUX ARRHYTHMO 2 (GmLUX2) both <span style="font-style: italic;">in vitro</span> and <span style="font-style: italic;">in vivo</span>. Although GmJMJ19/20 bind to histones, they lack conventional histone demethylase activity. Rather, GmJMJ19/20 function as endopeptidases that specifically cleave histone H3 peptides at unmethylated lysine 27 residues, in a manner independent of Fe²⁺ and α-ketoglutarate, the cofactors required for typical JmjC enzymes. Structural modeling supports the occlusion of the catalytic pocket that prevents access to methylated substrates. The simultaneous knockout of <span style="font-style: italic;">GmJMJ19</span>/<span style="font-style: italic;">20</span> significantly delays flowering time. Comparative transcriptomic analyses reveal that the GmJM19/20-GmLUX2 module enhances <span style="font-style: italic;">GmFULc</span> expression via independent of the canonical evening complex. Haplotype analysis suggests that <span style="font-style: italic;">GmJMJ19</span> underwent selection during domestication, potentially contributing to soybean geographical adaptation.</span>