| Bacolod to Cagayan de Oro | 🇵🇭 🇵🇭 | 20h | 2GO Travel | 1 | year round |
| Bacolod to Iloilo | 🇵🇭 🇵🇭 | 1h to 1h 30m | 3 operators | 77 | year round |
| Batangas to Abra de Ilog | 🇵🇭 🇵🇭 | 2h 30m | Montenegro Shipping Lines | 21 | year round |
| Batangas to Bacolod | 🇵🇭 🇵🇭 | 25h | 2GO Travel | 1 | year round |
| Batangas to Calapan | 🇵🇭 🇵🇭 | 1h 10m to 3h | 5 operators | 147 | year round |
| Batangas to Caticlan | 🇵🇭 🇵🇭 | 8h to 11h | 3 operators | 14 | year round |
| Batangas to Iloilo | 🇵🇭 🇵🇭 | 17h | 2GO Travel | 1 | year round |
| Batangas to Odiongan | 🇵🇭 🇵🇭 | 9h to 10h | 3 operators | 10 | year round |
| Batangas to Puerto Galera | 🇵🇭 🇵🇭 | 1h to 2h | Montenegro Shipping Lines | 28 | year round |
| Batangas to Roxas City (Capiz) | 🇵🇭 🇵🇭 | 15h 30m to 18h | 2GO Travel, Starlite Ferries | 5 | year round |
| Bato (Leyte) to Ubay (Bohol) | 🇵🇭 🇵🇭 | 3h 30m | Medallion Transport | 7 | year round |
| Bulalacao to Caticlan | 🇵🇭 🇵🇭 | 3h 30m | FastCat | 7 | year round |
| Cagayan de Oro to Iloilo | 🇵🇭 🇵🇭 | 13h | 2GO Travel | 1 | year round |
| Cagayan de Oro to Jagna (Bohol) | 🇵🇭 🇵🇭 | 5h 30m to 6h | Cokaliong Shipping Lines, Lite Ferries | 14 | year round |
| Caticlan to Odiongan | 🇵🇭 🇵🇭 | 3h to 4h | 2GO Travel, Starlite Ferries | 5 | year round |
| Caticlan to Roxas (Oriental Mindoro) | 🇵🇭 🇵🇭 | 3h | Montenegro Shipping Lines, Starlite Ferries | 14 | year round |
| Caticlan to Roxas City (Capiz) | 🇵🇭 🇵🇭 | 5h | 2GO Travel | 2 | year round |
| Cebu to Cagayan de Oro | 🇵🇭 🇵🇭 | 8h to 12h 30m | 4 operators | 23 | year round |
| Cebu to Dapitan | 🇵🇭 🇵🇭 | 10h to 15h | Starlite Ferries, Cokaliong Shipping Lines | 6 | year round |
| Cebu to Davao | 🇵🇭 🇵🇭 | 20h 30m | 2GO Travel | 1 | year round |
| Cebu to Dipolog | 🇵🇭 🇵🇭 | 12h | Medallion Transport | 3 | year round |
| Cebu to Dumaguete | 🇵🇭 🇵🇭 | 4h 20m to 6h | OceanJet, Cokaliong Shipping Lines | 21 | year round |
| Cebu to General Santos | 🇵🇭 🇵🇭 | 47h 30m | 2GO Travel | 1 | year round |
| Cebu to Getafe (Bohol) | 🇵🇭 🇵🇭 | 1h 15m | OceanJet | 7 | year round |
| Cebu to Iligan | 🇵🇭 🇵🇭 | 14h 30m to 15h | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 6 | year round |
| Cebu to Iloilo | 🇵🇭 🇵🇭 | 12h to 14h 45m | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 8 | year round |
| Cebu to Larena (Siquijor) | 🇵🇭 🇵🇭 | 9h to 10h | Starlite Ferries, Lite Ferries | 6 | year round |
| Cebu to Lazi (Siquijor) | 🇵🇭 🇵🇭 | 10h | Trans-Asia Shipping Lines | 3 | year round |
| Cebu to Maasin (Southern Leyte) | 🇵🇭 🇵🇭 | 3h to 6h 30m | 3 operators | 18 | year round |
| Cebu to Masbate | 🇵🇭 🇵🇭 | 12h to 14h 45m | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 6 | year round |
| Cebu to Nasipit (Butuan) | 🇵🇭 🇵🇭 | 12h | Cokaliong Shipping Lines, Starlite Ferries | 7 | year round |
| Cebu to Ormoc | 🇵🇭 🇵🇭 | 3h to 7h | 4 operators | 35 | year round |
| Cebu to Ozamiz | 🇵🇭 🇵🇭 | 10h to 11h | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 8 | year round |
| Cebu to Palompon (Leyte) | 🇵🇭 🇵🇭 | 3h to 6h | OceanJet, Cokaliong Shipping Lines | 11 | year round |
| Cebu to Siquijor | 🇵🇭 🇵🇭 | 4h 20m | OceanJet | 7 | year round |
| Cebu to Surigao | 🇵🇭 🇵🇭 | 5h 30m to 10h | 3 operators | 14 | year round |
| Cebu to Tacloban | 🇵🇭 🇵🇭 | 5h to 9h 30m | Roble Shipping, Trans-Asia Shipping Lines | 10 | year round |
| Cebu to Tagbilaran | 🇵🇭 🇵🇭 | 2h to 4h | 6 operators | 64 | year round |
| Cebu to Tubigon | 🇵🇭 🇵🇭 | 1h to 2h | 3 operators | 35 | year round |
| Coron to El Nido | 🇵🇭 🇵🇭 | 3h 30m | Montenegro Shipping Lines, Jomalia Shipping | 14 | year round |
| Coron to Puerto Princesa | 🇵🇭 🇵🇭 | 13h | 2GO Travel | 1 | year round |
| Davao to Bitung (North Sulawesi) | 🇮🇩 🇵🇭 | | 2GO Travel | | year round |
| Davao to General Santos | 🇵🇭 🇵🇭 | 9h | 2GO Travel | 2 | year round |
| Dipolog to Zamboanga | 🇵🇭 🇵🇭 | 11h | 2GO Travel | 1 | year round |
| Dumaguete to Dapitan | 🇵🇭 🇵🇭 | 4h to 6h | 5 operators | 49 | year round |
| Dumaguete to Dipolog | 🇵🇭 🇵🇭 | 3h 30m to 6h | 3 operators | 15 | year round |
| Dumaguete to Siquijor | 🇵🇭 🇵🇭 | 40m to 2h | 3 operators | 35 | year round |
| Dumaguete to Tagbilaran | 🇵🇭 🇵🇭 | 2h | OceanJet | 14 | year round |
| Dumaguete to Zamboanga | 🇵🇭 🇵🇭 | 16h 30m | 2GO Travel | 1 | year round |
| Dumangas (Iloilo) to Banago (Bacolod) | 🇵🇭 🇵🇭 | 1h | FastCat, Starlite Ferries | 28 | year round |
| General Santos to Bitung (North Sulawesi) | 🇮🇩 🇵🇭 | | 2GO Travel | | year round |
| General Santos to Iloilo | 🇵🇭 🇵🇭 | 25h | 2GO Travel | 1 | year round |
| Iligan to Ozamiz | 🇵🇭 🇵🇭 | 2h | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 6 | year round |
| Iloilo to Puerto Princesa | 🇵🇭 🇵🇭 | 36h | Montenegro Shipping Lines | 1 | year round |
| Jagna (Bohol) to Nasipit (Butuan) | 🇵🇭 🇵🇭 | 8h to 12h | Lite Ferries, Cokaliong Shipping Lines | 6 | year round |
| Liloan (Southern Leyte) to Lipata (Surigao) | 🇵🇭 🇵🇭 | 3h to 3h 30m | Montenegro Shipping Lines | 21 | year round |
| Maasin (Southern Leyte) to Surigao | 🇵🇭 🇵🇭 | 2h to 4h | OceanJet, FastCat | 14 | year round |
| Manila (Pasay) to Puerto Princesa | 🇵🇭 🇵🇭 | 17h | 2GO Travel | 1 | year round |
| Manila to Bacolod | 🇵🇭 🇵🇭 | 21h | 2GO Travel | 3 | year round |
| Manila to Butuan (Masao) | 🇵🇭 🇵🇭 | 44h | 2GO Travel | 1 | year round |
| Manila to Cagayan de Oro | 🇵🇭 🇵🇭 | 39h | 2GO Travel | 2 | year round |
| Manila to Cebu | 🇵🇭 🇵🇭 | 24h | 2GO Travel | 2 | year round |
| Manila to Coron | 🇵🇭 🇵🇭 | 13h | 2GO Travel | 1 | year round |
| Manila to Davao | 🇵🇭 🇵🇭 | 61h | 2GO Travel | 2 | year round |
| Manila to Dipolog | 🇵🇭 🇵🇭 | 49h 30m | 2GO Travel | 1 | year round |
| Manila to Dumaguete | 🇵🇭 🇵🇭 | 55h | 2GO Travel | 1 | year round |
| Manila to General Santos | 🇵🇭 🇵🇭 | 48h | 2GO Travel | 1 | year round |
| Manila to Iloilo | 🇵🇭 🇵🇭 | 30h | 2GO Travel | 3 | year round |
| Manila to Ozamiz | 🇵🇭 🇵🇭 | 44h | 2GO Travel | 1 | year round |
| Manila to Tagbilaran | 🇵🇭 🇵🇭 | 33h | 2GO Travel | 1 | year round |
| Manila to Zamboanga | 🇵🇭 🇵🇭 | 48h 30m | 2GO Travel | 1 | year round |
| Matnog to Allen | 🇵🇭 🇵🇭 | 2h | 3 operators | 126 | year round |
| Matnog to Dapdap (San Isidro, Samar) | 🇵🇭 🇵🇭 | 1h 30m | FastCat | 14 | year round |
| Surigao to Dapa (Siargao) | 🇵🇭 🇵🇭 | 2h | Montenegro Shipping Lines | 14 | year round |
| Tagbilaran to Cagayan de Oro | 🇵🇭 🇵🇭 | 10h 30m to 11h 30m | Lite Ferries, Trans-Asia Shipping Lines | 6 | year round |
| Toledo (Cebu) to San Carlos (Negros) | 🇵🇭 🇵🇭 | 1h 30m to 2h | FastCat, Lite Ferries | 21 | year round |
| Zamboanga to Bongao (Tawi-Tawi) | 🇵🇭 🇵🇭 | 17h | Aleson Shipping Lines, Montenegro Shipping Lines | 4 | year round |
| Zamboanga to Isabela (Basilan) | 🇵🇭 🇵🇭 | 1h to 1h 30m | 4 operators | 56 | year round |
| Zamboanga to Jolo (Sulu) | 🇵🇭 🇵🇭 | 3h 30m to 9h | 3 operators | 18 | year round |
| Zamboanga to Lamitan (Basilan) | 🇵🇭 🇵🇭 | 1h 30m to 2h | Montenegro Shipping Lines, Aleson Shipping Lines | 14 | year round |
| Zamboanga to Sandakan (Sabah) | 🇲🇾 🇵🇭 | 16h | Aleson Shipping Lines | 1 | year round |
