Revealing the composition and role of rare and abundant microbial groups is crucial to understand ecosystem processes and function. In 2018, we characterized soil bacterial community, abundant (AMPs) and rare microbial populations (RMPs) with mineral fertilizer and mineral fertilizer combined with straw return under continuous maize (Zea mays L.) and soybean (Glycine max Merr.)-maize rotation systems in a Mollisol in Northeast China. The results showed that the effects of fertilization on total bacterial community, AMPs and RMPs were greater than cropping systems. The cropping systems had a stronger effect on α diversity of bacterial community than fertilization. The RMPs accounted for 50.1% of the relative abundance and contributed 64.3% to the community dissimilarity. The RMPs accounted for 96.7% of the amount of operational taxonomic units (OTUs), thus became the most important contributors to community diversity. The OTUs with lower relative abundance had a narrower niche range, indicating that rare OTUs were more easily affected by habitat uniqueness. The RMPs were important contributors to chemoheterotrophs and were more closely correlated with variations in soil functions than AMPs. Our results provided deep insight into the ecological role of RMPs, which is useful for rational management and improving agricultural ecosystem sustainability. [ABSTRACT FROM AUTHOR]