Here in the Bay State, there are two species of cottontail rabbits - the New England cottontail (Sylvilagus transitionalis) and the Eastern cottontail (Sylvilagus floridanus).
You cannot tell these rabbits apart by looking at them in the field. The differences can be determined with certainty only by skull characteristics and measurements and by DNA techniques.
Generally speaking, however, New England cottontails have slightly shorter ears (avg. 57mm) and smaller bodies (avg. 958 g) than Eastern cottontails (avg. 61mm and 1136 g).
New England cottontails have a black spot between the ears about 90% of the time (40% in Eastern). They lack a white spot on the forehead (Easterns have a spot 43% of the time). New England Cottontails typically (95%) have a black line on the front edge of the ear (Easterns 40%).
Historically, New England cottontails were present in all 14 counties of Massachusetts. Prior to 1930, this was the only cottontail species appearing among 59 reports, except for 7 from Nantucket where Eastern cottontails were introduced as early as the 1880s.
Between 1924 and 1941, however, at least 16,200 Eastern cottontails were imported from the mid-west and released. Another 4600 were raised at a state propagation facility and released.