The first DNA sequences obtained from arbuscular endomycorrhizal fungi are reported. They were obtained by directly sequencing overlapping amplified fragments of the nuclear genes coding for the small subunit rRNA. These sequences were used to develop a polymerase chain reaction primer (VANS1) that enables the specific amplification of a portion of the vesicular-arbuscular endomycorrhizal fungus small subunit rRNA directly from a mixture of plant and fungal tissues. The specificity of this primer for arbuscular endomycorrhizal fungi was demonstrated by testing it on a number of organisms and by sequencing the fragment amplified from colonized leek (Allium porum) roots. This approach, coupled with other molecular techniques, will facilitate rapid detection, identification, and possibly quantitation of arbuscular endomycorrhizal fungi.