Molecular recognition of 1-(2-octadecyloxycarbonylethyl)cytosine monolayers at the air-water interface to complementary guanosine bases in the subphase has been studied using infrared reflection-absorption spectroscopy. It is the first time that the exact sites in the cytosine rings involved in the triple hydrogen-bonding interaction between complementary base pairs cytosine and guanosine are distinguished with the in situ technique. It is shown that the cytosine rings undergo a flat-on orientation before molecular recognition to an end-on one after molecular recognition and that the alkyl chains are more tilted after molecular recognition. Further simulation calculation shows that the tilt angle of the alkyl chains in the monolayers undergoes a change from 20degrees with respect to the film normal before molecular recognition to 30degrees after molecular recognition, which indicates that the chain orientation is strongly influenced by the recognition interaction between the cytosine moieties in the monolayers and the complementary guanosine bases in the subphase.