Machine-transplanted rice (Oryza sativa L.) (MTR), water direct-seeded rice (WDSR), and dry direct-seeded rice (DDSR) are three important alternatives to traditional manual transplantation of rice. Weed infestation is a pervasive problem in all rice planting systems. The weed seedbanks under different rice planting systems have seldom been compared. Thus, we sampled weed seeds in fields employing MTR, WDSR, and DDSR consecutively for at least 5 yr in Wujin County, eastern China. Seeds of 26 companion weed species of rice, comprising 16 families, were observed. Most weed seeds, 82.5% in MTR, 75.3% in WDSR, and 81.7% in DDSR, were distributed in soil 0- to 10-cm deep. As soil depth increased, the seedbanks of total weeds, broadleaf weeds, grasses, and sedges all significantly decreased under the different rice planting systems, except for sedges under WDSR. The DDSR tended to maintain larger seedbanks of sedges and grasses, as well as some upland weeds, such as Digitaria sanguinalis (L.) Scop. and Eleusine indica Gaertn. The WDSR system contained the smallest weed seedbank overall but tended to have larger seedbanks of several weeds, such as Ammannia arenaria H. B. K. and Lindernia procumbens (Krock.) Philcox. Weedy rice and Cyperus difformis L. tended to maintain larger seedbanks in DSR fields. The MTR fields tended to have larger seedbanks of broadleaf weeds and some traditional rice weeds, with significantly lower richness of weed species in the seedbank. Therefore, to downsize the weed seedbank, WDSR or MTR should be employed rather than DDSR when possible. Moreover, the influences rotation of different rice planting systems on the weed seedbank merit more studies.