In plant ecology, characterising colonisation and extinction in plant metapopulations is challenging due to the non-detectable seed bank that allows plants to emerge after several years of absence. In this study, we used a Hidden Markov Model to characterise seed dormancy, colonisation and germination solely from the presence-absence of standing flora. Applying the model to data from a long-term survey of 38 annual weeds across France, we identified three homogeneous functional groups: (1) species persisting preferentially through spatial colonisation, (2) species persisting preferentially through seed dormancy and (3) a mix of both strategies. These groups are consistent with existing ecological knowledge, demonstrating that ecologically meaningful parameters can be estimated from simple presence-absence observations. These results indicate that such studies could contribute to the design of weed management strategies. They also open the possibility of testing life-history theories such as the dormancy/colonisation trade-off in natura.