Secret Room

Secret Rooms are a feature that was added to the game in PMU 7. They are areas in dungeons that can be accessed through entering golden stairs found on a dungeon floor. These stairs have a random chance of spawning on a floor and initially spawn hidden. The floors a Secret Room can spawn on and the rate of appearance varies on the dungeon. Not all dungeons have Secret Rooms, and Secret Rooms can only appear in randomly-generated dungeons. Fixed dungeons such as Friendship Forest will never have Secret Rooms. Secret Room stairs also cannot spawn on the last floor in dungeon or its given section.

Secret Rooms often reward players with a varying amount of Deluxe Boxes that can give items when opened at Xatu's Appraisal. However, some Secret Rooms also allow players to obtain rare, exclusive Pokémon.

List of dungeons with Secret Rooms
The following below lists the dungeons that contain Secret Rooms and their corresponding information.

Exbel

 * Thunderstorm Forest and Far Thunderstorm Forest - 4 boxes
 * Island Garden - 2 boxes
 * Honeydrop Meadow - Scyther (Dawn), Pinsir (Dusk)
 * Gritty Hollow - 2 boxes
 * Loch Lenile Cavern - Red Moon Spring (10F-19F), 2 boxes
 * Mt. Barricade - 5 boxes
 * Southern Sea - 4 boxes
 * Harmonic Tower - 3 boxes (50F-74F), 1 box and Bagon (75F+)

Winden

 * Winden Forest - 2 boxes
 * Sauna Cavern - 3 boxes
 * Snowveil Den - 2 boxes
 * Mt. Stormhold - 2 boxes
 * Sky Fortress paths - 2 boxes
 * Sky Fortress/Sky Garden - 4 boxes

Tanren

 * Rocky Shoreline - Basculin
 * Sunken Gardens - 1 box, Alomomola
 * Sunrise Temple - Larvesta egg
 * Tanren Graveyard - Mimikyu
 * Tanren Mines - 2 boxes
 * Tanren Mines Depths - 2 boxes
 * Tanren Basement - 4 boxes
 * Tanren Courtyard - 2 boxes, Spiritomb (Night)
 * Iceberg Cavern - Entrance to Iceberg Frigid Waters
 * Iceberg Frigid Waters - Clauncher (Dawn and day)
 * Iceberg Adrift - 2 boxes
 * Daydream Dream Grove - 2 boxes, Cresselia (31F+)
 * Nightmare Dream Grove - 2 boxes, Darkrai (31F+)
 * Undercity Catacombs - 2 boxes, Vullaby
 * Ancient Caustic Sewers - 2 boxes

Archford

 * Stark Volcanic Woods - Victini
 * Boggy Wastes - 4 boxes
 * Starlit Lagoon - 2 boxes
 * Inferno Volcano - 2 boxes
 * Seafloor Ruins - 2 boxes
 * Mysterious Jungle - 2 boxes
 * Mt. Moon - 2 boxes
 * Sandy Shallows - Pikachu
 * Murky Trench - 2 boxes

Pokémon
In certain Secret Rooms it is possible to spawn Pokemon with Honey. The Pokémon that spawn in these rooms are often rare Pokémon only in these areas. The spawnable Secret Room Pokémon are as follows:
 * Scyther - Honeydrop Meadow (Dawn only)
 * Pinsir - Honeydrop Meadow (Dusk only)
 * Bagon - Harmonic Tower
 * Basculin - Rocky Shoreline
 * Alomomola - Sunken Gardens
 * Clauncher - Iceberg Frigid Waters (Dawn and day only)
 * Cresselia - Daydream Dream Grove
 * Darkrai - Nightmare Dream Grove
 * Vullaby - Undercity Catacombs
 * Victini - Stark Volcanic Woods

Not all Pokémon are obtained through Honey, however.
 * Sunrise Temple - The player can obtain a Larvesta egg after going through a puzzle.
 * Tanren Courtyard - The player can use an Odd Keystone, only if it is night, on the stone well in its to spawn a recruitable Spiritomb.
 * Tanren Graveyard - The player can use a Worn Doll on the sparkling tiles to spawn a recruitable Mimikyu.
 * Sandy Shallows - You'll meet a surfing Pikachu who will then challenge you to a battle after the dialogue sequence and is recruitable.
 * Seafloor Ruins/Central - You can find a Secret Room wherein you can use Sea Dew to unlock a door leading to a platform to use a Wonder Egg and summon a recruitable Phione.

Red Moon Spring
The Red Moon Spring is a special Secret Room that was added to Loch Lenile Cavern. It serves a special purpose and a different layout then the common Secret Room. Instead of Deluxe Boxes or Honey spawns that are found in other Secret Rooms, the player can regenerate Fossil Pokémon using Fossils when the time of the day is night, similar to summoning Spiritomb.

The Fossils that can be obtained and revived in Red Moon Springs are as follows:
 * Helix Fossil (Omanyte) - Tanren Chambers/Water
 * Dome Fossil (Kabuto) - Crystal Ruins
 * Old Amber (Aerodactyl) - Mt. Skylift
 * Claw Fossil (Anorith) - Tanren Chambers/Bug
 * Root Fossil (Lileep) - Tanren Chambers/Grass
 * Armor Fossil (Shieldon) - Tanren Chambers/Steel
 * Skull Fossil (Cranidos) - Tanren Chambers/Rock
 * Plume Fossil (Archen) - Tanren Chambers/Fighting
 * Jaw Fossil (Tyrunt) - Tanren Chambers/Dragon, Dragon's Descent Depths

When you summon the Pokémon via the Fossil, it will be at level 25 with recruitment rate of 100%. Only one Fossil can be used per Red Moon Spring.