Background, aim, and scope Some environmental and ecological records from several islands of the Xisha Archipelago, South China Sea, have been reconstructed in our earlier study. However, little is known about history of the Qilianyu in the Xisha Islands so far. Zhaoshu and Beidao are the two typical coral islands in Qilianyu of the Xisha Archipelago. To reconstruct history of the two islands, chronology analysis is a prerequisite. Well-preserved seabird subfossils were recovered from the ornithogenic sediments. It is aimed to establish chronology for two sediment profiles collected from Beidao and Zhaoshu islands based on radiocarbon dating of seabird remains. Materials and methods Ornithogenic sediments were observed during our field investigations into the Qilianyu, Xisha Islands in the year 2015. Two sediment profiles, namely ZS2 and BD1,were collected and analyzed from Zhaoshu and Beidao islands, respectively. They are 94 cm (ZS2) and 137 cm (BD1) in length. Both the two profiles consisted of three sediment units. Similarity in lithology of the cores suggests that the two islands may have a similar history and be restricted by identical environmental factors. A large number of seabird subfossil remains, including guano particles, eggshells, fish scales and bones etc., were observed and recovered in the bulk ornithogenic sediments. These biological materials imply historical occupation of these islands by seabirds. Avian subfossils were separated from the bulk sediments, and bone samples were used to investigate island history via radiocarbon (~(14)C) analysis. Results ~(14)C ages increased with depth for each of the profiles, suggesting well-preservation of the sediments. The ~(14)C ages based on seabird remains are much younger than previously reported ~(14)C ages from carbonate materials, and this could be explained by secondary transport of the carbonates. Seabird-based ~(14)C ages reveal that the collected samples were accumulated within approximately the last 1000 years. Direct mathematic fitting, R-language based Bacon and Clam programs were employed to establish age-depth models of the two profiles. It is found that the age-depth model constructed by Bacon is more suitable for age-depth modelling than mathematic fitting models and Clam package model. Discussion The seabird subfossils in the bulk ornithogenic deposits reflect gradual accumulation of the sediments, as well as upward growth of the islands. According to the age-depth models for the two sediment profiles based on Bacon program package, it is found that the mean sedimentation rates of the two profiles within the last 1000 years are 0.86 mm·a~(-1) and 1.26 mm·a~(-1), respectively. This partly represents growth rates of the islands, which are significantly lower than the rate of sea level rising in the present day. This implies a potential threat to island ecosystem. In addition, the initial activity of seabirds on the Zhaoshu Island is no later than AD 11721290, and the first occupation of the Beidao Island by birds began no later than AD 9841140. Conclusions The ornithogenic sediments from Zhaoshu and Beidao islands have been well-preseved and are ideal materials for studying history of the islands. Age-depth models based on Bacon program are suggested for further studies concerning the two islands. Mean upward growth rate of the islands within the last millennium is lower than that of present sea level rise. Seabird began to inhabit Qilianyu at approximately 9001000 years ago. Recommendations and perspectives Chronology is essential in island history study of the Xisha Archipelago. The established chronology in the present study provides basis for further climatic, environmental and ecological records of the two islands. This study also suggests a potential threat from sea level rise on the islands, as the rising rate of sea level is greater than growth rates of the two islands, implying an underlying risk of global warming on reef islands.