The allelopathic effect of aqueous and ethanol extracts of different plant parts (i.e. root, stem, leaf and fruit) of the invasive weed Solanum rostratum were investigated. Leaf extracts exhibited the most potent inhibitory activity against various indicator species including Amaranthus retroflexus and Poa annua; the aqueous extract of leaves completely suppressed seed germination of test plants, while the ethanol extract of leaves inhibited root growth of test plants by 53~93%. The ethanol extract of leaves and stems of S. rostratum was further partitioned by petroleum ether, chloroform, ethyl acetate and butanol, which were subsequently subjected to phytotoxic bioassay against A. retroflexus and P. annua at 5 mg/ml. Chloroform and butanol extracts showed the strongest phytotoxic activity, inhibiting root growth of test species by 71~94%. Our results indicated that the major active allelochemicals were present in two fractions, the chloroform and butanol extracts of leaves and stems of S. rostratum. The indirect allelopathic effects of S. rostratum were also evaluated. We found that invasion of S. rostratum did not affect soil moisture, soil pH and electrical conductivity significantly; however, invasion of S. rostratum enhanced activities of several soil enzymes. Furthermore, pyrosequencing analysis revealed that invasion of S. rostratum triggered a significant shift in the composition and structure of soil fungi. We suggest that S. rostratum potentially releases bioactive compounds into the environment which can not only directly inhibit neighboring plant growth but also indirectly alter soil properties to facilitate its invasion success.