Conjunctions play a crucial role in the construction of a coherent mental representation by signaling coherence relations between clauses, especially for second language users. By using event-related potentials (ERPs), this study aimed to investigate how different conjunctions ("so," "and," "although," or a "full stop") affect the interpretation of a following ambiguous pronoun for both native and non-native speakers, in sentences such as "Lily disappointed Nina, so she ...". ERP results showed that relative to "so," "and," and "full stop" sentences, the pronoun in "although" clauses elicited a larger "Nref" (sustained negativity) response in both native (L1) readers and second language (L2) readers, irrespective of whether the verb in the first clause biased towards a particular noun phrase (NP) referent. Moreover, larger "Nrefs" to pronouns were seen in L2 than L1 readers when clauses were connected by "so," "although" or a "full stop." Additionally, larger "Nref" responses were evoked by pronouns in NP2- than NP1-biased conditions when the clauses were connected by the conjunction so or when sentences contained no overt conjunctions ("full stop"). These findings indicate that different conjunctions exert different modulating effects on resolving referential uncertainty/ambiguity. Relative to native speakers, non-native speakers are more likely to encounter referential uncertainty when the sentences are conjoined by conjunctions with more complex semantics.