The enzymes of the isoflavonoid pathway produce isoflavones, which have multiple functions in defence and symbiosis. Recently, we identified known and novel homologues of several of these enzymes in the soybean genome sequence. In the present study, we have investigated the transcript levels of the isoflavone 7-O-glucosyltransferase (GmIF7GT) and 2-hydroxyisoflavanone dehydratase (HIDH) gene homologues in soybean seedling organs (shoot tips, unifoliate leaves, unifoliate nodes, epicotyls, cotyledons, cotyledonary nodes, hypocotyls and roots) as well as flowers, seeds and whole pods using real-time reverse-transcription polymerase chain reaction (real-time RT-PCR). In addition, the transcript levels were also measured in three cell layers of the soybean pod (exocarp, mesocarp and endocarp) dissected using laser capture microdissection (LCM) at two different developmental stages. Statistical analysis has shown that the transcript level of a less known gene homologue of isoflavone 7-O-glucosyltransferase (GmIF7GT4) is significantly higher (about 11-fold) in the roots than the well known gene homologue (GmIF7GT1) and the other less known homologues. It was also shown that the transcript levels of the less known gene homologue of 2-hydroxyisoflavanone dehydratase (HIDH2) do not differ from those of the well known homologue (HIDH1).