Desert riparian forest is an important vegetation type of inland river valleys in the arid zone, and dominates the structure and function of riparian ecosystems, as well as the landscape vegetation patterns. The occurrence and development of riparian forests are closely related to river runoff, while stand composition and distribution patterns are affected strongly by the hydrological regime of rivers. Riparian forests commonly proliferate on initially bare flooded surfaces. Flooding was found to have an overriding effect on riparian plant communities, and riparian ecosystems in arid regions exhibit shifting patterns of vegetation in response to periodic flooding. Desert riparian forest dominated by Populus euphratica has a centralized distribution in the Tarim River Basin, China, with highest abundance in the middle reaches of the Tarim River. In recent decades, desert riparian forest has been degraded severely in the lower reaches of the Tarim River, in part owing to alteration of natural flow regimes and suppression of fluvial processes. The flooding control violates inherent laws of riparian forest development, and consequently natural regeneration of riparian forests is checked. Extensive efforts have been made in recent years to restore riparian forests by regulating the hydrological regime according to natural flow regimes. Riparian forest rehabilitation and stability primarily depend on whether the dominant species regenerates successfully. Therefore, P. euphratica plays an important role in rehabilitation of natural riparian forests. Populus euphratica can reproduce both sexually and vegetatively. As sexual reproduction is important to maintain intrapopulation genetic diversity, investigation of seedling recruitment is critical for effective forest conservation. In most riparian plant species, such as P. euphratica, adult individuals mainly depend on groundwater to exist, while seed germination and early establishment are always related to surface runoff. Seedling establishment is an important life-history phase of floodplain plants in relation to drought stress. While distribution, community composition and structure have been the subject of considerable research, few studies have investigated the contribution of flooding to riparian forest establishment. With the objective of verifying whether the relationship between seedling establishment and flooding could explain the spatial pattern and community dynamics of riparian forests, in this study the species composition, quantity, diversity and growth status of seedlings were compared in three habitats, namely floodplain, forest floor, and forest gap. Field investigation of seedling recruitment after flooding was carried out from June 2008 to August 2009 in the middle reaches of the Tarim River. Seedling recruitment mainly depended on flooding, with no seedlings developing in the sample plots that had not been flooded. Flooding reduces soil salinity and represents a combination of temporal and quantitative water supply for both germination and growth of riparian plants such as P. euphratica. The seedling density and species diversity on the floodplain were distinctly higher than those in the other two habitats in the seasonally flooded area. Light availability was a critical factor influencing the level of seedling recruitment. High illumination promoted seedling recruitment and the accumulation of biomass.