Increasing studies have shown the importance of intraspecific trait variation (ITV) on ecological processes. However, the patterns and sources of ITV are still unclear, especially in the propagules of coastal vegetation. Here, we measured six hypocotyl traits for 66 genealogies of Kandelia obovata from 26 sites and analyzed how ITV in these traits was distributed across geography and genealogy through variance partitioning. We further constructed mixed models and structural equation models to disentangle the effects of climatic, oceanic, and maternal factors on ITV. Results showed that size‐related traits decreased along increasing latitudinal gradients, which was mainly driven by positive regulation of temperature on these traits. By contrast, ITV of shape trait was unstructured along latitudinal gradients and did not show any dependence among environmental variables. These findings indicate that propagule size mainly varied between populations, whereas propagule shape mainly varied between individuals. Our study may provide useful insights into the ITV in propagule from different functional dimensions and on a broad scale, which may facilitate mangrove protection in light of ITV.