Abstract Body: Left ventricular non-compaction cardiomyopathy (LVNC) is a rare heart condition characterized by excessive trabeculae and intertrabecular recesses in the left ventricle of the heart. It is believed to be caused by abnormal trabecular compaction process, which involves trabecular remodelling to form a thick myocardial wall. Embryonic trabeculae consist of bipotent progenitors that differentiate into the ventricular conduction system (VCS) and contractile cardiomyocytes, yet it remains to be further understood how the pathways involved in trabecular cell specifications play a role in the compaction process. Here we present two transcription factors, Iroquois homeobox 3 (Irx3) and Irx4, playing antagonistic and cooperative roles during trabecular specification and maturation, thereby facilitating proper ventricular compaction. Our single-cell RNA sequencing analysis revealed that the differentiation of trabecular cells into VCS cells was accompanied by increased Irx3 but decreased Irx4 expression. In addition, we found that the loss of Irx4 led to both an increased expression level of Irx3 and an expansion in the number of Irx3-expressing cells. Conversely, the loss of Irx3 resulted in an upregulation of Irx4 expression within VCS cells. Next, to investigate the functional importance of the antagonistic relationship between Irx3 and Irx4 in trabecular differentiation, we generated Irx3 and Irx4 compound knockout (KO) mice and examined the structure and function of their hearts. Notably, unlike Irx3 KO hearts showing normal ventricular myocardium, Irx4 KO hearts exhibited mild LVNC, and Irx3 and Irx4 double knockouts (Irx3/4dKO) hearts displayed severe LVNC. Multiome sequencing of E14.5 ventricles revealed that Irx3/4dKO ventricles contained an increased number of trabecular cells, expressing higher levels of cell proliferation markers and altered trabecular identity genes, compared to littermate controls. Collectively, our results demonstrate that balanced antagonism between Irx3 and Irx4 is crucial for establishing trabecular identity. This highlights the importance of proper differentiation of trabeculae into the VCS and non-VCS contractile cells during ventricular compaction, thereby preventing noncompaction cardiomyopathy.