The serotonin-1A (5-HT1A) receptor is strongly implicated in major depression and other affective disorders due to its negative regulation of serotonin neurone firing rates. Behavioural and clinical studies have repeatedly reported that the -1019G allele carries a high susceptibility for affective disorders. However, the underlying pathophysiology remains unknown. Here, we employed a genetic neuroimaging strategy in 99 healthy human subjects to explore the effect of serotonin-1A receptor polymorphism on brain resting-state functional connectivity (FC). We used functional magnetic resonance imaging, along with a seed-based approach, to identify three main brain networks: the default mode network (DMN), the salience network (SN) and the central executive network. We observed a significant decrease in the FC of the DMN within the dorsolateral and ventromedial prefrontal cortices in G-carriers. Furthermore, compared with the C-homozygote group, we observed decreased FC of the SN within the ventromedial prefrontal cortex and subgenual anterior cingulate cortex in the G-carrier group. Our results indicate that 5-HT1A receptor genetic polymorphism modulates the activity of resting-state FC within brain networks including the DMN and SN. These genotype-related alterations in brain networks and FC may provide novel insights into the neural mechanism underlying the predisposition for affective disorders in G allele carriers.