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== Tujuan ==
{{main|Daftar bandar udara tujuan Merpati Nusantara Airlines}}
CGK Jakarta - MKW Manokwari PP.
CGK Jakarta - DJJ Jaya Pura PP.
CGK Jakarta - KNO Medan PP.
CGK Jakarta - PDG Padang PP.
CGK Jakarta - SUB Surabaya PP.
CGK Jakarta - BTH Batam PP.
CGK Jakarta - UPG Makassar PP.
HLP Jakarta - UPG Makassar PP.
Hlp Jakarta - SUB Surabaya PP.
CGK Jakarta - LOP Lombok PP.
CGK Jakarta - PNK Supadio Kal.Bar PP.
CGK Jakarta - PKY Tiilik Riwut Kal.Teng PP.
CGK Jakarta - BDJ Syamsudin Noor PP.
CGK Jakarta - AAP Aji Pangeran Tumenggung PP.
CGK Jakarta - TRK Juwata Kaltura PP.
CGK Jakarta - DPS Denpasar PP.
CGK Jakarta - AMQ Mutiara Sulteng PP.
CGK Jakarta - GTO Jalaludin Gorontalo PP.
CGK Jakarta - MCD Sam Ratulangi Sulut PP.
CGK Jakarta - TTE Sultan Babullah Ternate PP.
CKG Jakarta - PLM Palembang PP.
CKG Jakarta - MKW Rendani PaBar PP.
CGK Jakarta - DPS Denpasar PP.
CGK Jakarta - BPN Balikpapan PP.
CGK Jakarta - MDC Manado PP.
UPG Makassar - DJJ Jaya Pura PP.
UPG Makassar - DPS Denpasar PP.
UPG Makassar - BPN Balikpapan PP.
UPG Makassar - SUB Surabaya PP.
UPG Makassar - MKW Manokwari PP.
UPG Makassar - BTH Batam PP.
UPG Makassar - MDC Manado PP
UPG Makassar - MJU Tampa Padang Sulbar PP.
UPG Makassar - MKW Rendani PaBar PP.
UPG Makassar - AMQ Mutiara Sulteng PP.
UPG Makassar - TTE Sultan Babullah Ternate PP.
UPG Makassar - MCD Sam Ratulangi Sulut PP
UPG Makassar - GTO Jalaludin Gorontalo PP
UPG Makassar - KDI Haluoleo Sulengg PP.
UPG Makassar - AMQ Pattimura Ambon PP.
UPG Makassar - BDJ Syamsudin Noor PP.
UPG Makassar - KOE El Tari NTT PP.
SUB Surabaya - AMQ Pattimura Ambon PP.
SUB Surabaya - BPN Balikpapan PP.
SUB Surabaya - YIA Yogyakarta PP.
SUB Surabaya - UPG Makassar PP.
SUB Surabaya - DJJ Jaya Pura PP.
SUB Surabaya - PKY Tiilik Riwut Kal.Teng PP.
KNO Medan - PLM Palembang PP.
KNO Medan - PDG Padang PP.
KNO Medan - PKY Pekan Baru PP.
KNO Medan - TXE Takengon/B.M PP.
KNO Medan - BTH Batam PP.
MKW Manok Wari - DJJ Jaya Pura PP.
== Armada ==
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