BackgroundWhile polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies,Ludwigiasect.Isnardia(comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies ofIsnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa.ResultsPhylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings onL. repensandL. sphaerocarpawere consistent with earlier studies;L. arcuatawas reported as a multi-origin taxon here, and an additional evolutionary scenario ofL. sphaerocarpawas uncovered, both for the first time. Furthermore, estimatedIsnardiaTMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations ofIsnardiataxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows amongIsnardiataxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported.ConclusionsThe present research gives new perceptions of the reticulate evolution and dynamic nature ofIsnardiaand points to gaps in current knowledge about allopolyploid evolution.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40529-023-00387-8.