The Fc alpha/mu receptor (Fcα/μR, CD351) is a receptor that has dual specificity for IgA and IgM. Its second extracellular domain (EC2) has an Ig variable region-like structure and is predicted to be the ligand binding domain. EC2 is homologous to the first Ig-like domain (D1) of polymeric Ig receptor (pIgR) and has three complementarity-determining region (CDR)-like loops. A peptide that includes the CDR1-like loop region has been found to be responsible for IgA and IgM binding. However, whether the CDR2- and CDR3-like loops of EC2 contribute to ligand binding has remained unclear. In this work, we made three chimaeric receptors composed of the hFcα/μR backbone but having the CDR1-, CDR2- and CDR3-like loops of EC2 replaced by their counterpart loops from human pIgR D2, which itself does not bind IgA or IgM. Flow cytometry and confocal microscopy analysis showed that substitution of either the CDR1- or the CDR2-like loop abrogated IgA and IgM binding, indicating that both the CDR1- and the CDR2-like loops were important for ligand binding. In comparison, substitution of CDR3-like loop resulted in significant loss of IgM binding but has only a small negative effect on IgA binding. In addition, site-directed mutagenesis of the three CDR-like loops showed that residues Val29, Arg31, Asn54, Gln55, Glu98, Asn99 and Asn100 were involved in both IgA and IgM binding, and substitution of Glu98 within the CDR3-like loop increased IgA binding but decreased IgM binding.