Agricultural ecosystems are vulnerable to biological invasions. There are a total of 239 invasive alien species in a variety of agricultural ecosystems in China. Among them, 155 species are plants, 55 are animals and 29 are microbes. The number of invasive alien species decreases from south to north, and from east to west in China. Invasive alien plant species are generally introduced intentionally, while animals and microbes are mainly unintentionally introduced. Among these invaders, 45.04% have a geographical origin in the Americas, 22.90% in Europe, and 16.41% in Asia. Of these species, 64.85% and 66.53% occur in vegetable gardens (including greenhouses) and orchards, respectively, while 34.31%, 23.85% and 6.28% occur in summer-harvested crop dry land, autumn-harvested crop dry land and paddy field, respectively. Among these 239 invaders, 17 plant species, 10 animals and 7 microbes are noxious pests which, we feel, deserve closer management attention. Currently, chemical control is the principal approach to managing these species in agricultural ecosystems. However, long-term application of pesticides has led to pesticide resistance in some invasive species, with 51 of the 239 invasive alien species reported as exhibiting pesticide-resistant populations worldwide. Therefore, more attention should be paid to management which integrates biological control, ecological measures, agronomic means and quarantine. We suggest that research into the following issues would be fruitful: patterns and mechanisms of and trends in biological invasions in agricultural ecosystems, origin sources and invasion pathways, influences of biological invasions and pesticide resistance on successions of pest communities, and biological invasions caused by transgenic crops.