To conserve threatened farmland species requires an estimate of the representation of their habitats within protected areas, especially in countries with inadequate mechanisms for protecting and managing habitats outside of protected areas. We conducted a gap analysis to evaluate the conservation status of suitable habitats for two threatened farmland bird species - corncrake (Crex crex) and lesser grey shrike (Lanius minor) - within the networks of national protected areas (NPAs) and important bird areas (IBAs) in Serbia. We determined the distribution of suitable habitats using MaxEnt based on climate, topography and land-cover variables. We found that the proportion of suitable habitats within the NPAs is very low (12.31% and 2.04% for the corncrake and lesser grey shrike, respectively), although it is significantly higher for both species within IBAs (25.86% and 9.91%, respectively). Upland farmland habitats (preferred by corncrake) are better represented within both networks (especially IBAs) than lowland habitats (preferred by lesser grey shrike). Our spatially explicit distribution models identify suitable habitats within and beyond the NPAs and IBAs that require monitoring and appropriate conservation measures. The low representation of suitable habitats within these networks is an obstacle to the conservation of both species and other farmland birds in Serbia.