The association between terrestrial plants and arbuscular mycorrhizal (AM) fungi is one of the most widespread mutualistic plant-fungus interactions in natural and cropping systems. We studied the effect of different plant densities (70,000 and 100,000 plant ha-1) on species diversity and community structure of AM fungi associated with maize (Zea mays L.) in a long-term crop production experiment established in Martonvásár, Hungary. Based on the differences in small subunit (SSU)/18S ribosomal genes nested-PCR procedure was used to identify groups of AM fungi that are active in the colonization of maize roots. Shannon-Wiener diversity index of AM fungi were 1.43 ± 0.37 and 1.31 ± 0.50 at 70,000 plant ha-1 and 100,000 plant ha-1 respectively. All of sequence types we found belonging to the Glomus clade. Besides Glomus A fungi, only the members of the Glomus B group occurred, however at significantly lower frequency. There were differences in the phylogenetic group composition of AM fungi demonstrating the effect of different plant densities on the diversity of arbuscular mycorrhizal fungi.