Waterlogging tolerance of tropical cordage fiber crops is an important agricultural subject in northeast Thailand, because they are often grown in dry-wet transition period as pre-rice crops. Since root anatomical characteristics are often considered to be important traits determining waterlogging tolerance of plants, we examined root anatomy of three fiber crops that are different in waterlogging tolerance one another. Seedlings of three cordage fiber crops, Hibiscus cannabinus (kenaf, cv. KhonKaen60), Hibiscus sabdariffa (roselle, Thai kenaf, cv. NonSoong2) and Corchorus olitorius (jute, cv. KhonKaen1), were grown in tall beakers of 1000 ml vermiculite with 40% v/v (control) and 80% v/v (waterlogging) water contents. It is known that the H. cannabinus cultivar is tolerant to waterlogging while other two species (C. olitorius, H. sabdariffa) cultivars are sensitive to waterlogging from soil-grown pot experiments in northeast Thailand. Ten days after sowing, freehand cross-sections of taproot (i.e., primary root) were made with 1 cm increments from the root tip along root axis followed by staining by toluidine blue O (0.01%) for light and fluorescence microscopy. Only H. cannabinus formed aerenchyma in cortex of the taproot under waterlogging condition. The aerenchyma of waterlogged H. cannabinus first appeared at 3 cm from the root tip and developed up to the base of taproot. The formation of aerenchyma in H. cannabinus roots may contribute to the waterlogging tolerance. Casparian bands were found in both endodermis and exodermis of taproot in all the three species. However, formation of exodermal Casparian bands was not stable, and they were restricted to the basal part of taproot in H. sabdariffa and C. olitorius. Waterlogging treatment suppressed formation of Casparian bands, particularly in exodermis.