- Al'Taieu
- Capital city of the Zilart.
- Altepa
- Home of Zeid after the Crystal War.
- Attowha Chasm
- Where Prishe and Ulmia meet Shikaree Z.
- Bastok
- A republic formed by Galkas and Humes. It started as a mining and fishing town, then flourished with technological advances after the San'dorian civil war. They developed trade routes with the San'doria and Windurst. It was the first great nation to be refitted for airship service. San'doria and Windurst soon followed.
- Battalia Downs
- Resting place of Lightbringer after the Crystal War.
- Cape Riverne
- Cape of Tavnazian safehold.
- Castle Zvahl
- Castle of the Shadow Lord.
- Davoi
- Site of the launch of the San'dorian civil war. Original site of lightbringer. Controlled by orcs during and following the Crystal War.
- Delkfutt Reactor
- Reactor key to opening the gates of paradise.
- Delkfutt's Tower
- Where the Gigas retreated to after the failed preemptive strike on Jeuno. The site of last remaining Zilart.
- Dragon King Birthplace and Monastery
- Taken over by orcs during Crystal War.
- Drogaroga's Spine
- One of the pillars used by Zilart to gain access to paradise.
- Dyanmis
- The world of dreams, created and guarded by Diabolos. Where the Shadow Lord's spirit rests.
- Eastern Empire
- The empire Tenzen serves. It is mentioned in the game, but not revealed. It is being enveloped by emptiness. Declared war on Jeuno at the end of Chains of Promathia.
- Elshimo
- Island home of the Mithra. Site of a pirate base after the Crystal War.
- Eventide
- A chamber created by Yve'noile if the gates to paradise were ever open.
- Fei'Yin
- Palace created for the two Zilart princes oversee the project to open the gates of paradise. The dawn maidens and Kuluu overloaded it, causing the Meltdown. Became an orc stronghold.
- Full Moon Fountain/Well
- Water well from the ancient Kuluu tribe. Bestowed the power of magic unto the Tarutaru, and gave the first Star Sybil the vision of the future.
- Garilage Citadel
- Site of a battle between Yagudo and San'dorian knights. The knights were building a large tunnel for the Tarutaru to escape through, but the Yagudo attacked and collapsed the tunnel just before it was finished. Formerly a temple when San'doria controlled the region.
- Ghelsba
- Territory annexed by orcs during and following the Crystal War.
- Heaven's Tower of Windurst
- A central point of the Kuluu canals discovered under Windurst by Karaha-Baruha.
- Horotoro Ruins
- Ruins where summoning was discovered. The first Tarutaru settlers discovered it.
- Jeuno
- A fishing town, developed by Bastok to the North. Due to their location as the main intersection of the kingdoms they grew powerful and broke off into their own Grand Duchy of Jeuno shortly before the Crystal War. They ballooned with trade and industry, and soon took Bastok's place as most powerful of nations. They have been secretly building armored air ships since the first was made and used in the Crystal War.
- Junger Forest
- Prince Fellenant fled here after his escape from prison.
- Konschat Highlands
- Key site of two battles between Bastok and San'doria.
- Kuftal Tunnel
- Site where Werei was searched for.
- Kuzotz
- Original home of the Galka. The anticans forced them out to the land that would come to be known as Bastok.
- La'Thiene Plateau
- Where Tenzen called Carbuncle
- Marquisate of Tavnazia
- The second Elvaan kingdom. It started as a small peninsula at the western edge of the Quon continent. Orcs took this land over in the Crystal War (this is the intro video scene). During the battle, a massive explosion caused the landing holding the peninsula to the continent to sink into the sea. Though it was a devastating loss for the forces of Tavnazia, it was more devastating for the beastmen, and was considered the turning point of the war. The explosion was later found to be caused by Rochefogne activating Lightbringer in the tunnels below Tavnazia while escorting the royal family to safety.
- Mhaura
- Joint city of the Mithra and Tarutaru.
- Mistalle
- Elvaan place.
- Movalpolos
- Capital of Moblins.
- Norg
- Pirate headquarters.
- Northlands
- Once a lush forest, turned into barren wasteland by the Meltdown.
- Northern Quon Continent
- This continent's forests are the home for orcs.
- Odin's Gate
- Gateway into Tarutaru terrirtory.
- Ordelle's Cave
- Site where King Raigegue's dethroing was to take place.
- Pso'Xja
- Ruins of the Kuluu. Has power of the slumbering gods. Selh'tus was sighted here.
- Quifim Island
- Home to a power core used by the Zilart to gain access to paradise. Later became the site of the most devastating raid by the kindred. Located near Jeuno.
- Ro'Maeve
- Gateway of the gods, access point to Tul'ia.
- Sacrarium
- Old temple where Promathia can be contacted. Home to undead. It was originally intended to be used to open the gates of paradise and ask Altana to lift the curse, but then the goal changed to studying the advanced artifacts of the ancients and attempting to bring Altana into our world. This ended when the Crystal War began.
- San'Doria
- The primary kingdom of the Elvaan. It desired to conquer all the lands of Vana'diel, but fell to Bastok and Windurst. Then fell into civil war. The nation is now in a state of decline.
- Sarutabaruta
- Surrounding grassland of Windurst. Outer defense of Windurst.
- Sauromugue Champaign
- Land conquered by the Elvaan San'doria. During the Crystal War, this was the site of a large tunnel used to help the Tarutaru escape from the Yagudo during the Crystal War. The orcs informed the Yagudo that this tunnel was being formed and they ambushed the Elvaan just before its completion and the tunnel failed, killing countless San'dorian knights.
- Selbina
- A fishing town, developed by Bastok in the south. They brought in more profit than Jeuno at first.
- Shrouded Maw
- Gateway to Dynamis.
- Southern Quon
- This region's swamps are the home for the quadav.
- Tavnazian Stronghold
- Last refuge of Tavnazian escapees, where survivors still live.
- Temple of Uggalepih
- Site where the Kuluu and dawn maidens would strike against Zilart.
- Temple of Yhoator
- Gilgamesh happened here once and received a clue to the past of the Zilart, involving the Zilart Princes.
- Tower of Kam'Lanaut
- Kam'Lanaut's home base.
- Tu'Lia
- A.K.A. the celestial nexus. It is a floating city designed as a monument to Zilart greatness. It still floats in orbit above Vana'diel and was the site of the final confrontation between the three heroes and Eald'narche. Afterwards, it lies inert in space.
- Windurst
- Kingdom of the Tarutaru and Mithra.
- Xarcabard
- Home base of the Shadow Lord.