Intensively cropped wheat (Triticum aestivum L.), rice (Oryza sativa L.), and maize (Zea mays L.) systems cover 30 million hectares of the region’s best agricultural land and provide over 80% of Asia’s cereal needs. However, the rate of production gains from conventional breeding for staple food crops has slowed from 2.9% (Green Revolution era) to 1.9% in less developed countries (LDCs), with gains frequently being offset by environmental stresses. In response to environmental changes and the availability of inputs, the rice-maize cropping system has become increasingly important in Asia. However, the impact of an anaerobic/aerobic cropping system on pest and disease complexes is largely unknown. The objective of this paper is to highlight pest management issues that could emerge as the area planted to a rice-maize cropping system increases. A review of the major pests associated with maize and rice found that at least 8 nematode, 18 diseases, and 71 insect species are common to both crops. This list of overlapping pest species is even larger when one considers minor pests associated with each crop. The groups of pests most likely to increase in importance are soil pests (white grubs and nematodes), armyworms (Spodoptera spp.), stem borers (Chilo spp., Sesamia spp.), storage pests (Sitophilus spp.). Diseases that may become more important include stalk rots (Erwinia chrysanthemi pv. Chrysanthemi and Gibberella zeae), root rots (Cochliobolus sativus) and banded leaf and sheath blight (Rhizoctonia solani). The interaction of these biotic stresses against the backdrop of climate change will also be discussed as will management issues such as insect resistant management strategies for regions where both Bt maize and rice are commercially available.