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flydubai will continue to operate from Terminal 2 with select flights from Terminal 3 and Al Maktoum International Airport (DWC), and Emirates from Terminal 3, Dubai International Airport. You should check in based on the operating carrier and not the marketing carrier. The terminal number is clearly mentioned at the time of booking and on your e-ticket or booking confirmation (only for Dubai).
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Emirates marketed flights on flydubai operated flights will use the 2000 to 2499 series. flydubai marketed flights on Emirates operated flights will use the 6000-6999 series.