Over the past few decades, major advances have been made in identifying the origins of cardiac cells from developing embryos. In particular, the discovery of the first heart field (FHF) and the second heart field (SHF), led us to understand how diverse lineages and different anatomical structures of the heart arise during cardiogenesis. However, it remains unknown how the two heart fields are specified and segregated, a fundamental step toward understanding heart formation and developing pluripotent stem cell (PSC)-based therapeutic strategies. Here, we generated 3D organoids with mouse PSCs that harbor green and red fluorescent protein (GFP and RFP) reporters under the control of the FHF marker Hcn4 and the SHF marker Tbx1, respectively. We demonstrate how GFP+ cells and RFP+ cells appear from two distinct areas of mesodermal cells and develop in a complementary fashion, similar to the in vivo process. Consistently, these populations exhibit a high degree of similarities with FHF/SHF cells isolated from early embryos, determined by RNA-sequencing analysis. Through a series of bioinformatics approaches, we found that Bmp and Wnt are among the most differentially regulated pathways in the two populations. Importantly, an increased activity of Bmp or Wnt signaling resulted in selective induction of GFP+ or RFP+ cells from mesodermal cells, enabling us to generate heart field-specific cells from PSCs. We further found that FHF/SHF cells can be distinguished and isolated by the surface proteins CD184 and EphA2. This study provides fundamental insights into understanding the specification of two cardiac origins that enable generation of chamber-specific populations for studying heart field/chamber-specific heart disease in cell culture.