The JR Group contains seven railway companies, including JR East, which is the biggest private railway in the Tokyo area. Tokyo Metro is the biggest subway/rapid transit system in the Tokyo area. Tokyo Metro trains run underground most of the time, while JR trains usually run above ground.

In Japan, particularly Tokyo, you can distinguish between JR (Japan Rail) and Metro/Subway lines by their logos and signage patterns. JR lines are represented by a square icon containing two letters (e.g., "JY" for the Yamanote Line) and always feature the green "JR" logo at station entrances. JR lines are mostly above ground and are the only ones covered by the nationwide Japan Rail Pass. In contrast, Metro and Subway lines (Tokyo Metro and Toei) use a circle icon with a single letter (e.g., "G" for the Ginza Line). Metro lines are almost entirely underground and require separate tickets or "IC cards" like Suica/Pasmo. When using Google Maps in 2026, JR lines are usually shown as solid colored lines, while subways may be dashed or have a different visual style. If you are standing at a large station like Shinjuku, look at the floor or overhead signs: yellow signs often point to JR, while brightly colored circles point to the various subway lines.