Abstract We present Ca–CN–CH–NH photometry for the well-known globular cluster (GC) M3 (NGC 5272). We show new evidence for two M3 populations with distinctly different carbon and nitrogen abundances, seen in a sharp division between CN-weak and CN-strong red-giant branches (RGBs) in M3. The CN-strong population shows a C–N anticorrelation that is a natural consequence of the CN cycle, while the CN-weak population shows at most a very weak C–N anticorrelation. Additionally, the CN-weak population exhibits an elongated spatial distribution that is likely linked to its fast rotation. Our derived metallicities reveal bimodal distributions in both populations, with 〈Fe/H〉 ≈ −1.60 and −1.45, which appear to be responsible for the discrete double RGB bumps in the CN-weak population and the large range. From this discovery, we propose that M3 consists of two GCs, namely C1 (23%, 〈Fe/H〉 ≈ −1.60) and C2 (77%, 〈Fe/H〉 ≈ −1.45), each of which has its own C–N anticorrelation and structural and kinematical properties, which are strong indications of independent systems in M3. The fractions of the CN-weak population for both C1 and C2 are high compared to Galactic GCs but they are in good agreement with GCs in the Magellanic Clouds. We suggest that M3 is a merger remnant of two GCs, most likely in a dwarf galaxy environment, and accreted to our Galaxy later in time. This is consistent with recent proposals of an ex situ origin for M3.