Abstract Heavy metal-contaminated land is increasingly becoming an important environmental, health, economic, and planning issue in Pakistan. The unplanned disposal of industrial effluent from tannery, for example, has resulted in a many fold increase in chromium (Cr) in the land near a tannery. This study was undertaken to compare the total and the DTPA-available Cr contents in the soil and the roots and leaves of tree species growing on it with those on the nearby noncontaminated reference site at Kala Shah Kakoo, Panjab, Pakistan. A very reduced plant cover on the tannery effluent-contaminated site was noted and there was a sharp boundary between the polluted and nonpolluted reference sites, suggesting a strong selection pressure. Polluted soil contained considerable higher amounts of Cr as compared to the reference soil but no correlation was found between Cr contents in the dried plant tissue and the total DTPA-extractable Cr. Roots of all the three tree species, i.e. Dalbergia sissoo, Acacia arabica, and Populus euroamericana, growing on both the contaminated as well reference site possessed arbuscular mycorrhizal fungal (AMF) infection in their roots and AMF propagules in the associated rhizospheres. D. sissoo and A. arabica roots were also studded with nitrogen-fixing rhizobial root nodules, while those of P. euroamericana possessed AMF as well as ectomycorrhizal infections. The dual infection would encourage mineral nutrition, including Cr. AMF community varied, i.e. trees growing on the reference site were exposed to a wide variety of AMF such as Glomus, Scutellospora, and Acaulospora, whereas those on the contaminated site contained only Gigaspora spp. in their mycorrhizospheres, suggesting a selection pressure. Typical Glomus infection patterns in the roots of D. sissoo growing on the contaminated soil but absence of spores of Glomus spp. in the associated rhizospheres indicate the potential error of using AMF spores to extrapolate the root infection. High Cr contents adversely affected the size, diversity, and species richness of AMF as measured by Shannon–Weiner index. The potential of mycorrhizae in protecting the host plant against the harmful effect of heavy metals and in phytoremediation of the Cr-polluted soil is discussed.