New Bark Town is located in southeastern Johto. It's a quaint town where the wind blows and tells of impending change.

Other than being connected to Route 29 in the west, it is also the town that must be passed through to reach Tohjo Falls, Victory Road, and Indigo Plateau, via Route 26 and Route 27.

Cherrygrove City is located in south-central Johto. Though the city has no Gym, it is frequently passed through by Pokémon Trainers on their way to Violet City from New Bark Town. Passersbys refer to it as "a city where you can smell small flowers and a sea breeze" as the ocean borders it to the west.

Violet City is an old village located in central Johto. Pokémon Trainers often come to Violet City in order to win the Zephyr Badge from the Violet Gym Leader, who specializes in Flying-type Pokémon. The city has three entrances, one from the east via Route 31, one from the south via Route 32, and one from the west via Route 36.

Azalea Town is a small, isolated town located on the southern peninsula of the Johto region. The town is best known for being the residence of Kurt, a custom Poké Ball creator who makes Poké Balls out of Apricorns. He lives in the northwest portion of town on the east edge of Ilex Forest. Azalea features other notable locations as well, such as the Slowpoke Well, and as such, Slowpoke can be found around the town. The town has two entrances, Route 33 to the east and Ilex Forest to the west.

Pokémon Trainers must journey to Azalea Town in order to win the Hive Badge from the Azalea Gym Leader who specializes in Bug-type Pokémon.

Ilex Forest is a dense forest located in southern Johto, directly west of Azalea Town. The forest's trees are so close together that all light is blocked out, and the forest seems to be in a perpetual night. These trees are used to make charcoal.

There is a Shrine for the guardian of the forest, Celebi.

Goldenrod City is a sprawling metropolis located in western Johto. It is the largest city in the region, rivaling Celadon City, the largest city in Kantō. Goldenrod City is the fifth largest city in the Pokémon world, behind Hoenn's Mauville City, Unova's Castelia City and Nimbasa City, and Kalos's Lumiose City. Goldenrod is the center of the region's economy and telecommunications. Major attractions for Trainers include the Goldenrod Radio Tower, the city's Department Store, Game Corner, Name Rater, Magnet Train, Global Terminal and Normal-type Gym.

The National Park, along with the Pokéathlon Dome, is located north of Goldenrod off Route 35 while the Pokémon Day Care is just south of the city on Route 34.

The National Park is a location in Johto. It is located to the north of Goldenrod City, between Route 35 and Route 36. It's a spacious and beautiful park that's connected to the Pokéathlon Dome.

The Pokéathlon Dome is a location in Johto, west of the National Park. It is the place where Pokéathlon competitions are held. Outside of the building, many Trainers can be seen with their Pokémon, practicing for the Pokéathlon's various competitions. A woman on the west side will give away an Apriblender to those who have an Apricorn Box, and afterwards she will sell Aprijuice.

Ecruteak City is an old-fashioned city located in northern Johto, situated in the woods between tall Mt. Mortar and the open fields near Johto's western shores.

As with many of the larger cities in the Pokémon world, Ecruteak has a Pokémon Gym that specializes in Ghost-type Pokémon.

Ecruteak is known as a historical and mythical city; fittingly, its buildings all feature traditional Japanese architecture, while the tallest building in the city, and perhaps all of Johto, is the ten-story Bell Tower in the city's northeast corner, built nearly a millennium ago. The city is known as being a centerpoint of the Legendary Pokémon native to the Johto region, with the great Ho-Oh once being said to have roosted atop the Bell Tower, and having created three Legendary beasts of the Pokémon who perished when the Brass Tower burned down.

Mt. Mortar is a large cave in Johto with three entrances on Route 42. Part of the large range of mountains north of the Johto region, it is known to be a confusing maze-like area with an interior cave known as the Waterfall Cave.

Olivine City is located on the Johto coast, near Ecruteak City and Cianwood City. Olivine is a major port city and is the home of the Glitter Lighthouse. The Glitter Lighthouse guides ships to the harbor as well as the S.S. Aqua connecting it to the port city in its sister region, Vermilion City in Kantō.

Pokémon Trainers often come to Olivine City in order to win the Mineral Badge from Gym Leader who specializes in Steel-type Pokémon.

Cianwood City is located in on the far western edge of Johto, apparently on a totally different landmass than the rest of the region. Due to Cianwood City being at a dead end location in the Johto region, it was not a popular destination. However, it became a notable destination due to the addition of the Safari Zone located to the west of the city. A Fighting-type Gym can also be found on this island.

Tales of Lugia and the whirlpools it creates circulate among the sailors that stop in this port town.

Mahogany Town is a small town in northern Johto where ninjas once resided in what eventually became the Team Rocket HQ. There are three exits out of town. To the west is Route 42, to the east is Route 44, and to the north is Route 43, which leads directly to the famous Lake of Rage.

Pokémon Trainers must come to Mahogany Town in order to win the Glacier Badge from the Mahogany Gym Leader who specializes in Ice-type Pokémon. Mahogany is a quiet, relaxed town, and has no Poké Mart. Instead, there is a shop used by Team Rocket as a base. After Team Rocket is defeated, it is converted into a store run by a little old lady.

Blackthorn City, a mysterious mountain village cut into a rock face, is located in northeast Johto.

Pokémon Trainers often come to Blackthorn City in order to win the Rising Badge from the Blackthorn Gym Leader, who specializes in Dragon-type Pokémon. Many famous Dragon-type Trainers, including Clair and Lance, come from Blackthorn City. According to a resident in Blackthorn, most Trainers in the city actually end up being Dragon-type specialists because of the Dragon's Den in the area, and because the local Gym Leader is a Dragon-type Trainer.