Whereas resting state BOLD (blood oxygenation-level dependent) functional MRI (fMRI) has been widely used to assess functional connectivity between cortical regions, the laminar specificity of such measures is poorly understood. This study aims to determine (a) whether the resting state functional connectivity (rsFC) between two functionally related cortical regions varies with depth, (b) the relationship between layer-resolved tactile stimulus-evoked activation pattern and inter-layer rsFC pattern between two functionally distinct but related areas 3b and 1, and (c) the effects of spatial resolution on rsFC measures. We examined the inter-layer rsFC between somatosensory areas 3b and 1 of squirrel monkeys under anesthesia using tactile stimulus-driven and resting state BOLD acquisitions at sub-millimeter resolution. Consistent with previous observations in the areas 3b and 1, we detected robust stimulus-evoked BOLD activations with foci confined mainly to the upper layers (centered at 21% of the cortical depth). By carefully placing seeds in upper, middle and lower layers of areas 3b and 1, we observed strong rsFC between superficial and middle layers of these two areas. The layer-resolved activation patterns in areas 3b and 1 agree with their inter-layer rsFC patterns, and are consistent with the known anatomical connections between layers. In summary, using BOLD rsFC pattern we identified an inter-layer inter-areal microcircuit that shows strong intrinsic functional connections between superficial and middle layer somatosensory areas 3b and 1 of monkeys. RsFC can be used as a robust invasive tool to probe inter-layer cortico-cortical microcircuits.