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This work is an attempt to critically analyze the correlation between great deep-focus undersea earthquake and possible ionospheric anomalies. The significant TEC (total electron content) temporal and spatial anomalies were detected over the epicenter of 2007 <i>M</i><i>_w</i>7.5 Jakarta–Java earthquake, and they coincide well with the striking plasma anomalies in the ionosphere in situ observed by the LEO (low Earth orbit) satellite. The localization and synchronization of the disturbances during the earthquake suggest that these ionospheric anomalies are highly related to this large undersea earthquake. In order to identify this correlation, we made efforts to distinguish seismo-associated signals from large electromagnetic noise due to solar and geomagnetic activities, natural non-seismic sources and known artificial signals. Nevertheless, the difficulties of this work should be recognized and approached with caution. This special (deep-focus and undersea) case study here provides us with valuable information on the study of lithosphere–atmosphere–ionosphere (LAI) coupling process and reminds us that deep-focus undersea seismic events need to be treated more carefully and discreetly in the future.