The derivation of functional cardiomyocytes (CMs) from human embryonic stem cells (hESC) represents a unique way of studying human cardiogenesis, including the development of CM subtypes. In this study, we investigated the development and organization of CMs derived from hESCs (hESC-CMs) and examined how the expression of CM subtypes correspond to human in vivo cardiogenesis. Beating clusters were used to determine cardiac differentiation, which was evaluated by the expression of cardiac genes GATA4 and TNNT2 and subcellular localization of GATA4 and NKX2.5. Sharp electrode recordings to determine action potentials (AP) further revealed spatial organization of intra-clustal CM subtypes (i.e complex clusters). Nodal-, atrial- and ventricular-like APs morphologies were detected within distinct regions of complex clusters. The ability of different CM subtypes to self-organize was documented by immunohistochemical analyses and a differential spatial expression of β-III tubulin, Myosin light chain 2v (MLC-2V) and α-smooth muscle actin (α-SMA). Further, all hESC-CM subtypes formed expressed primary cilia, which are known to coordinate cellular signalling pathways during cardiomyogenesis and heart development. Finally, the β-III tubulin specific localised expression is suggested to represent a new marker for nodal CMs. This study expands our understanding of CM specialization and intra-clustal CM subtype organization, improving the foundation for studying regulatory pathways for spatial and temporal CM differentiation during human cardiogenesis.