The G protein-coupled receptor APJ/Aplnr has been widely reported to be involved in heart and vascular development and disease, but whether it contributes to organ left-right patterning is largely unknown. Here, we show that in zebrafish,
aplnra/b
coordinates organ LR patterning in an
apela/apln
ligand-dependent manner using distinct mechanisms at different stages. During gastrulation and early somitogenesis,
aplnra/b
loss of function results in heart and liver LR asymmetry defects, accompanied by disturbed KV/cilia morphogenesis and disrupted left-sided
Nodal/spaw
expression in the LPM. In this process, only
aplnra
loss of function results in KV/cilia morphogenesis defect. In addition, only
apela
works as the early endogenous ligand to regulate KV morphogenesis, which then contributes to left-sided
Nodal/spaw
expression and subsequent organ LR patterning. The
aplnra-apela
cascade regulates KV morphogenesis by enhancing the expression of
foxj1a
, but not
fgf8
or
dnh9
, during KV development. At the late somite stage, both
aplnra
and
aplnrb
contribute to the expression of
lft1
in the trunk midline but do not regulate KV formation, and this role is possibly mediated by both endogenous ligands,
apela
and
apln
. In conclusion, our study is the first to identify a role for
aplnra/b
and their endogenous ligands
apela/apln
in LR patterning, and it clarifies the distinct roles of
aplnra-apela
and
aplnra/b-apela/apln
in orchestrating organ LR patterning.