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Understanding and controlling decoherence in open quantum systems is of fundamental interest in science, while achieving long coherence times is critical for quantum information processing. Although great progress was made for individual, isolated systems, and electron spin resonance (ESR) of single spins with nanoscale resolution has been demonstrated, the construction of complex solid-state quantum devices requires ultimately controlling the environment down to atomic scales, as potentially enabled by scanning probe microscopy with its atomic and molecular characterization and manipulation capabilities. Consequently, the recent implementation of ESR in scanning tunneling microscopy (STM) represents a milestone towards this goal and was quickly followed by the demonstration of coherent oscillations, tunable dipolar and exchange couplings and access to nuclear spins with real-space atomic resolution. Atomic manipulation even fueled the ambition to realize first artificial atomic-scale quantum devices. However, the current-based sensing inherent to this method limits coherence times. Here, we demonstrate pump-probe ESR atomic force microscopy detection of electron spin transitions between non-equilibrium triplet states of individual pentacene molecules. Spectra of these transitions exhibit sub-nanoelectronvolt energy resolution, allowing local discrimination of molecules that only differ in their isotopic configuration. Furthermore, the electron spins can be coherently manipulated over tens of microseconds, likely not limited by the detection method but by the molecular properties. Single-molecule ESR atomic force microscopy can be combined with atomic manipulation and characterization, and thereby paves the way for atomically well-defined quantum components with long coherence times and local quantum-sensing experiments.