Microglia are known to play critical roles in healthy brain development and function, as well as the neuropathology underlying a range of brain diseases. Despite the growing evidence for a role for microglia in affective regulation and mood disorders, relatively little is known regarding how variation in microglia status relates to individual differences in emotionality. Using a selective breeding model based on locomotor response to novelty, we have generated rat lines with unique temperamental phenotypes that reflect broad emotional traits: low responder rats (bLRs) are novelty-averse and model a passive coping style, whereas high responder rats (bHRs) are highly exploratory and model an active coping style. To identify a possible functional role of microglia in these phenotypes, we administered minocycline, an antibiotic with potent microglia inhibiting properties. We found changes in emotional and social behaviors in bLRs, with no discernable effects in bHRs. Using detailed anatomical analyses, we went on to explore the nature of baseline differences in hippocampal microglia populations associated with the divergent temperaments. Interestingly, we found that although bHRs and bLRs had comparable total numbers of hippocampal microglia, selective breeding was associated with a shift in the morphological features of these cells. Specifically, microglia from bLRs were characterized by a hyper-ramified morphology, with longer processes and more complicated branching patterns than microglia from bHRs. This morphology is thought to reflect an early stage of microglia activation and suggests that microglia from bLRs may be in a reactive state even when animals are not overtly stressed or challenged. Taken together, our results provide novel evidence linking variation in inborn temperament with differences in the baseline morphological status of microglia cells and highlight the importance of considering the role of microglia not only in acute responses to stress but also in shaping enduring characteristics of emotionality.