Trust is a basic component that shapes a group in social animals and is known to vary with social contexts. Many studies have demonstrated the power of ascribed identity (e.g., ethnicity, gender) upon trust behaviors among human beings. However, few studies have investigated how acquired identity (e.g., political party) may influence one’s trust to another person and the corresponding neural mechanisms. To address this issue, we enrolled 58 healthy adults who share different political identities, defined by their presidential choices in the 2012 Taiwan presidential election (i.e., KMT vs. DPP supporters), to participate a repeated binary trust game experiment while undergoing fMRI scan. Each participant was informed that two types of partner (same and different political identity) were included in the present study. At the behavioral level, we found that political identity modulated cooperative decisions, as reflected in higher frequency of trust decisions when participants were interacting with a partner having the same political identity. At the neural level, our fMRI analyses for the same political identity trials in which the participants’ partner defected compared with trials in which the partner reciprocated showed significant hemodynamic signal change in the brain regions implicated in emotional processing (anterior insula), mentalizing (temporoparietal junction), and self-regulatory control (dorsolateral prefrontal cortex). In contrast, participants exhibited greater activation in the striatum (reward learning) in response to different political identity trials in which the partner reciprocated compared with trials in which the partner defect. More importantly, the aforementioned result patterns were observed only for one group, but not the other, even though both groups showed strong sign for in-group preferences.  The current results therefore highlight the complexity about how acquired social identities render its influence upon interpersonal trust interactions, which cannot be solely explained by in-group favoritism proposed by the social identity theory.