Background Human APJ receptor (APJR), a rhodopsin family G-Protein Coupled Receptor (GPCR), activated by isoforms of peptide ligand apelin causing potent inotropic effect, is involved in cardiac function, angiogenesis and maintenance of fluid homeostasis. APJR is expressed in various organs e.g., heart, brain, kidney, muscles, etc. Hence, problems in APJR signaling lead to severe dysregulation in the pathophysiology of an organism. Methods Based on multiple sequence alignment of receptors from various organisms, we observe a large number of conserved residues in the extracellular side. Mutational studies including calcium mobilization, receptor internalization and ERK1/2 phosphorylation assays were performed. Results Stimulation of APJR and its mutants with apelin-13 led to mutation-dependent variation in receptor activation, intracellular Ca2+ rise, and its subsequent downstream signaling. The mutant 183MDYS186-AAAA in ECL2 showed Gi-biased signaling while 268KTL270-AAA in ECL3 showed Gq biasing. C281A mutant in ECL3 was deficient in all assays. Conclusion Conserved residues in the ECL2 of APJR are key for ligand binding, activation mechanism, and selective downstream signaling. Additionally, we demonstrate that Cys281 (in ECL3) mediated disulfide linkage is important for ligand recognition and receptor activation. General significance This work explains the importance of extracellular loop domains in ligand binding, receptor activation and downstream signaling of human APJR. © 2016 Elsevier B.V.