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This paper elucidates one interacting aspect of two problematic issues in Japanese grammar: the functional differences between the nominative marker GA and the topic marker WA, and the referential identity of ellipted subjects. My analysis shows that the interaction of WA and GA in complex sentences has an analogous property to switch-reference systems which determine the identity of ellipted subjects; GA in subordinate clauses signals Different Subject, and WA in all loci Same Subject. This syntactic finding is further evaluated in the light of non-syntactic features, some of which can override the interpretation created by these particles. Statistically in examining texts, however, over 90% of ellipted subjects in complex sentences are successfully identified solely by WA and GA.