This information came from Wikipedia and maybe out of date as routes change so frequently.
Aegean Airlines 
Seasonal charter: Heraklion International Airport
Seasonal charter: Heraklion International Airport Aer Lingus Dublin
DublinSeasonal charter: London-Gatwick
Aigle Azur Algiers, Béjaïa, Constantine, Oran, Sétif
Algiers, Béjaïa, Constantine, Oran, SétifSeasonal: Funchal, Tlemcen
Air Algérie Algiers, Annaba, Batna, Biskra, Constantine, Oran, Sétif, Tlemcen
Algiers, Annaba, Batna, Biskra, Constantine, Oran, Sétif, Tlemcen Air Arabia Maroc Casablanca
Casablanca Air Austral Saint-Denis de la Réunion
Saint-Denis de la Réunion Air France Amsterdam [ends 2 September 2012], Bordeaux, Nice, Paris-Charles de Gaulle, Toulouse, Tunis
Amsterdam [ends 2 September 2012], Bordeaux, Nice, Paris-Charles de Gaulle, Toulouse, Tunis Air France operated by Air Corsica Ajaccio, Bastia
Ajaccio, BastiaSeasonal: Figari
Air France operated by Airlinair Clermont-Ferrand, Florence, Limoges, Marseille, Milan-Malpensa, Montpellier, Paris-Orly, Pau, Stuttgart, Toulouse
Clermont-Ferrand, Florence, Limoges, Marseille, Milan-Malpensa, Montpellier, Paris-Orly, Pau, Stuttgart, Toulouse Air France operated by Brit Air Barcelona, Brest, Budapest, Caen, Düsseldorf, Lille, Nantes, Nice, Prague, Rennes, Rome-Fiumicino, Strasbourg
Barcelona, Brest, Budapest, Caen, Düsseldorf, Lille, Nantes, Nice, Prague, Rennes, Rome-Fiumicino, StrasbourgSeasonal: Bastia
Air France operated by Régional Amsterdam, Basel/Mulhouse, Biarritz, Bologna, Brussels, Clermont-Ferrand, Gothenburg-Landvetter [begins 17 September 2012], Lorient, Metz/Nancy, Milan-Malpensa, Pau, Stuttgart, Venice-Marco Polo
Amsterdam, Basel/Mulhouse, Biarritz, Bologna, Brussels, Clermont-Ferrand, Gothenburg-Landvetter [begins 17 September 2012], Lorient, Metz/Nancy, Milan-Malpensa, Pau, Stuttgart, Venice-Marco PoloSeasonal: Naples, Southampton
Air Malta Seasonal: Malta
Seasonal: Malta Air Méditerranée Seasonal: Agadir, Athens, Bodrum, Chlef, Corfu, Dakar, Djerba, Fuerteventura, Heraklion, Ibiza, Jijel, Malaga, Marrakech, Monastir, Palma de Mallorca, Tenerife-South
Seasonal: Agadir, Athens, Bodrum, Chlef, Corfu, Dakar, Djerba, Fuerteventura, Heraklion, Ibiza, Jijel, Malaga, Marrakech, Monastir, Palma de Mallorca, Tenerife-South Air Transat Seasonal: Montreal-Trudeau
Seasonal: Montreal-Trudeau Airlinair La Rochelle, Poitiers
La Rochelle, Poitiers Armavia Seasonal: Yerevan
Seasonal: Yerevan Austrian Airlines operated by Tyrolean Airways Vienna
Vienna BMI Regional Manchester
Manchester British Airways London-Heathrow
London-Heathrow Brussels Airlines Brussels
Brussels Brussels Airlines operated by Flybe Brussels
Brussels Camair-Co Douala, Yaoundé
Douala, Yaoundé Chalair Aviation Le Havre
Le Havre Croatia Airlines Seasonal: Split
Seasonal: Split EasyJet Agadir, Barcelona, Berlin-Schönefeld [ends 16 March 2013], Berlin-Brandenburg [begins 17 March 2013], Bordeaux, Brest, Brussels, Casablanca, Edinburgh, Lisbon, London-Gatwick, London-Stansted, Madrid, Marrakech, Milan-Malpensa, Nantes, Nice, Pisa, Porto, Prague, Rome-Fiumicino, Toulouse, Venice-Marco Polo
Agadir, Barcelona, Berlin-Schönefeld [ends 16 March 2013], Berlin-Brandenburg [begins 17 March 2013], Bordeaux, Brest, Brussels, Casablanca, Edinburgh, Lisbon, London-Gatwick, London-Stansted, Madrid, Marrakech, Milan-Malpensa, Nantes, Nice, Pisa, Porto, Prague, Rome-Fiumicino, Toulouse, Venice-Marco PoloSeasonal: Ajaccio, Bastia, Biarritz, Bristol, Ibiza, Olbia, Palermo
Emirates Dubai [begins 5 December 2012
Dubai [begins 5 December 2012Hex'Air Castres, Rodez
Castres, Rodez Iberia operated by Air Nostrum Madrid
MadridSeasonal: Palma de Mallorca
Jetairfly Agadir, Casablanca, Marrakech
Agadir, Casablanca, Marrakech KLM operated by KLM Cityhopper Amsterdam [begins 3 September 2012]
Amsterdam [begins 3 September 2012] Lufthansa Berlin-Tegel [ends 16 March 2013], Berlin-Brandenburg [begins 17 March 2013], Düsseldorf, Frankfurt
Berlin-Tegel [ends 16 March 2013], Berlin-Brandenburg [begins 17 March 2013], Düsseldorf, Frankfurt Lufthansa Regional operated by Eurowings Düsseldorf
Düsseldorf Lufthansa Regional operated by Lufthansa CityLine Düsseldorf, Munich
Düsseldorf, Munich Onur Air Seasonal: Izmir
Seasonal: Izmir Royal Air Maroc Casablanca, Marrakech
Casablanca, Marrakech Scandinavian Airlines Copenhagen
Copenhagen Scandinavian Airlines operated by Cimber Air Copenhagen
Copenhagen Swiss International Air Lines operated by Helvetic Airways Zürich
Zürich Swiss operated by Swiss European Air Lines Zürich
Zürich Syphax Airlines Sfax
Sfax TAP Portugal Lisbon
Lisbon TAP operated by Portugália Lisbon
Lisbon TAROM Bucharest-Henri Coanda
Bucharest-Henri Coanda Transaero Airlines Moscow-Domodedovo
Moscow-Domodedovo Transavia.com France Djerba, Monastir
Djerba, MonastirSeasonal: Heraklion
Tunisair Djerba, Monastir, Tunis, Tozeur
Djerba, Monastir, Tunis, Tozeur Turkish Airlines Istanbul-Atatürk
Istanbul-Atatürk Vueling Barcelona, Palma de Mallorca
Barcelona, Palma de Mallorca WOW air Reykjavik-Keflavik
Reykjavik-Keflavik XL Airways France Seasonal: Catania, Punta Cana
Seasonal: Catania, Punta CanaFlights, airlines to and from Lyon Airport
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