I recently traveled to Shillong on work and by a reference from a friend stayed at a delightful facility styled as "Aerodene Cottage" in a locality called Lower Cleve Colony. It is a family-run guest house with very reasonable rates (INR 2500 per nite) and it was very tastefully furnished and had all modern conveniences. For me especially the free wi-fi was a boon. It is run personally by the owner, a well-traveled lady who takes a lot of interest in the comfort of the guests. The cleanliness and class are quite evident. The managers can arrange local sightseeing and adventure tours and there was talk of a small spa coming up soon. The facility is in the heart of town, yet set apart and peaceful, with loads of greenery and private garden spaces.
All in all, I recommend this place for any discerning traveler who would like to have an authentic "cottage" experience at Shillong and would cherish a personal touch of comfort and service.
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Stay well, Roger (NYC)