The PAIR2 gene is required for homologous chromosome synapsis at meiosis I in rice (Oryza sativa L.) and encodes a HORMA-domain protein that is homologous to Saccharomyces cerevisiae HOP1 and Arabidopsis ASY1. Immunocytological and electron microscopic analyses indicate that PAIR2 proteins associate with axial elements (AEs) at leptotene and zygotene, and is removed from the AEs of arm regions when homologous chromosomes have been synapsed. Immunocytology against a centromeric histone H3 variant revealed that PAIR2 remains at centromeres until diakinesis, by which time the homologous centromeres had already been synapsed. However, neither precocious segregation of sister chromatids nor kinetochore dysfunction is observed, and AEs are normally assembled in the mutant. In the pair2-null mutant, homologous chromosome synapsis is completely eliminated. This study provides the first description of AE-associated protein in monocot plants and indicates that PAIR2 plays an essential role in promoting homologous chromosome synapsis. However, PAIR2 does not play a role in AE formation, sister chromatid cohesion at centromeres or kinetochore assembly in meiosis I of rice.