This paper presents a comparison of two reduced-order, sequential and variational data assimilation methods: the SEEK filter and the R-4D-Var. A hybridization of the two, combining the variational framework and the sequential evolution of covariance matrices, is also preliminarily investigated and assessed in the same experimental conditions. The comparison is performed using the twin-experiment approach on a model of the Tropical Pacific domain. The assimilated data are simulated temperature profiles at the locations of the TAO/TRITON array moorings. It is shown that, in a quasi-linear regime, both methods produce similarly good results. However the hybrid approach provides slightly better results and thus appears as potentially fruitful. In a more non-linear regime, when Tropical Instability Waves develop, the global nature of the variational approach helps control model dynamics better than the sequential approach of the SEEK filter. This aspect is probably enhanced by the context of the experiments in that there is a limited amount of assimilated data and no model error.