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Non-native aquatic Ludwigia species from a polyploid complex are among the world’s most problematic invasive plants. These emergent, floating-leaved species respond to disturbance through fragmentation of shoots and/or rhizomes, spreading rapidly by hydrochorous dispersal and posing challenges for invasive plant management. While recruitment of clonal aquatic plant species from shoot fragmentation is well documented, regeneration from rhizome bud banks, although common, often is overlooked. It is further unclear how interactions among ploidy and resource availability influence regeneration success of rhizome fragments. We conducted a full factorial experiment in aquatic mesocosms to compare trait responses of Ludwigia congeners differing in ploidy (diploid, decaploid) grown from clonal rhizome fragments under contrasting soil nutrient availability (low, high). Similar to previous work with shoot fragments, the diploid congener had a higher relative growth rate and produced more biomass than the decaploid during this establishment stage of growth. High growth rates and biomass production were associated with greater rhizome N and P and reduced investment in below-ground structures. Comparing these results to previous shoot fragment studies with Ludwigia, rhizome fragments appear to have much greater growth potential, suggesting that management strategies should minimize disturbance to prevent fragmentation and dispersal of below-ground structures. Furthermore, rapid response to newly colonizing diploid invaders will be essential to minimizing spread, and reductions in nutrient loads to aquatic environments may be more effective towards controlling establishment of the diploid congener than the decaploid.