| 35 | 35 | Ocean Beach - Old Town | MTS |
| 14 | 14 | Grantville Trolley - Baltimore & Lake Murray | MTS |
| 235 | 235 | Downtown - Escondido Transit Center | MTS |
| 909 | 909 | Otay Mesa Transit Center - SWC at Otay Mesa | MTS |
| 961 | 961 | 24th St Transit Center - Encanto Trolley | MTS |
| 968 | 968 | 8th St Transit Center - Plaza Bonita | MTS |
| 934 | 934 | Iris TC Loop - Imperial Beach Clockwise | MTS |
| 18 | 18 | Grantville Trlly via Camino del Rio | MTS |
| 12 | 12 | 12th & Imperial - Skyline Hills | MTS |
| 936 | 936 | Spring Valley - SDSU | MTS |
| 4 | 4 | 12th & Imperial Trolley - Lomita Village | MTS |
| 27 | 27 | Pacific Beach - Kearny Mesa Transit Center | MTS |
| 41 | 41 | Fashion Valley - UCSD | MTS |
| 44 | 44 | Old Town - Kearny Mesa | MTS |
| 701 | 701 | H St Transit Center - Palomar St TC via Hilltop Dr | MTS |
| 888 | 888 | Jacumba - El Cajon | MTS |
| 928 | 928 | Fashion Valley - Kearny Mesa | MTS |
| 955 | 955 | National City - San Diego State University | MTS |
| 967 | 967 | 24th St Transit Center - Division & Ava | MTS |
| 816 | 816 | El Cajon TC - Cuyamaca College | MTS |
| 929 | 929 | 12th & Imperial - Iris Transit Center | MTS |
| 962 | 962 | 8th St Transit Center - Spring Valley | MTS |
| 709 | 709 | H St Transit Center - Otay Ranch Town Center | MTS |
| 892 | 892 | Borrego - El Cajon via Ranchita/Lake Henshaw | MTS |
| 875 | 875 | El Cajon Eastside Shuttle Counterclockwise | MTS |
| 120 | 120 | Downtown San Diego - Kearny Mesa Transit Center | MTS |
| AIR | Old Town to Airport Shuttle | SAN | |
| 11 | 11 | SDSU - Downtown San Diego | MTS |
| 202 | 202 | Super Loop - Clockwise | MTS |
| 945 | 945 | Rancho Bernardo Station - Poway | MTS |
| 530 | Green | El Cajon - 12th & Imperial | MTS |
| 520 | Orange | El Cajon - Courthouse | MTS |
| 992 | 992 | Airport/Downtown Shuttle | MTS |
| 204 | 204 | Super Loop - Judicial Dr. | MTS |
| 280 | 280 | Escondido Transit Center - Downtown | MTS |
| 105 | 105 | Old Town - University City | MTS |
| 833 | 833 | Santee Center - Parkway Plaza | MTS |
| 838 | 838 | East County Square - Viejas | MTS |
| 854 | 854 | Grossmont Transit Ctr -- Grossmont College | MTS |
| 921 | 921 | UTC - Miramar College Transit Station | MTS |
| 550 | Silver | Downtown Loop | MTS |
| COR | Coronado Ferry | MTS | |
| 932 | 932 | Iris Transit Center - 8th St. Transit Center | MTS |
| 891 | 891 | Borrego - El Cajon via Shelter Valley | MTS |
| 985 | 985 | UCSD Central Campus Station - Torrey Pines | MTS |
| 832 | 832 | Santee Center - NE Santee Loop Clockwise | MTS |
| 10 | 10 | Old Town - University/College | MTS |
| 88 | 88 | Old Town - Hotel Circle | MTS |
| 25 | 25 | Fashion Valley - Kearny Mesa TC | MTS |
| 31 | 31 | UTC - Mira Mesa | MTS |
| 9 | 9 | Old Town - Jewell & Garnet | MTS |
| 43 | 43 | Balboa Av TC - Kearny Mesa | MTS |
| 815 | 815 | El Cajon Transit Center - East Main St | MTS |
| 907 | 907 | Iris Transit Center - San Ysidro Counterclockwise | MTS |
| 894 | 894 | Morena/Campo - El Cajon | MTS |
| 856 | 856 | SDSU - Cuyamaca College | MTS |
| 906 | 906 | Iris Transit Center - San Ysidro Clockwise | MTS |
| 933 | 933 | Iris TC Loop - Imperial Beach Counterclock | MTS |
| 237 | 237 | Miramar College Transit Station - UCSD | MTS |
| 872 | 872 | El Cajon Shuttle Loop Counterclockwise | MTS |
| 2 | 2 | Downtown San Diego - 30th & Adams | MTS |
| 855 | 855 | Rancho San Diego - La Mesa | MTS |
| 834 | 834 | West Santee Loop | MTS |
| 944 | 944 | Sabre Springs Station - Poway | MTS |
| 7 | 7 | Downtown San Diego - University/College | MTS |
| 964 | 964 | Mira Mesa - Alliant University via MCTS | MTS |
| 510 | Blue | San Ysidro - UTC | MTS |
| 290 | 290 | Sabre Springs Station - Downtown | MTS |
| 60 | 60 | Euclid Av Transit Center - UTC via Convoy | MTS |
| 13 | 13 | Kaiser Hospital - 24th St Transit Center | MTS |
| 848 | 848 | El Cajon - Lakeside | MTS |
| 30 | 30 | Old Town - UTC via Pacific Beach | MTS |
| 965 | 965 | City Heights Shuttle | MTS |
| 28 | 28 | Old Town T.C. - Shelter Island | MTS |
| 705 | 705 | E St Transit Center - Plaza Bonita | MTS |
| 535 | Copper | Santee - El Cajon | MTS |
| 864 | 864 | El Cajon - East County Sq | MTS |
| 20 | 20 | Downtown - Rancho Bernardo Transit Station | MTS |
| 115 | 115 | El Cajon T.C. - SDSU T.C. | MTS |
| 916 | 916 | Oak Park-Emerald Hills Loop CW | MTS |
| 84 | 84 | Point Loma Shuttle | MTS |
| 707 | 707 | Otay Ranch Town Center - Southwestern College | MTS |
| 83 | 83 | Downtown San Diego - Old Town | MTS |
| 901 | 901 | Iris Transit Center - Downtown | MTS |
| 852 | 852 | University & 54th - Grossmont Transit Ctr | MTS |
| 904 | 904 | Coronado Shuttle | MTS |
| 905 | 905 | Iris Transit Center - Otay Mesa Transit Center | MTS |
| 712 | 712 | Palomar Transit Center - Southwestern College | MTS |
| 874 | 874 | El Cajon Eastside Shuttle Clockwise | MTS |
| 923 | 923 | Downtown to Point Loma | MTS |
| 225 | 225 | Downtown - Otay Mesa TC | MTS |
| 8 | 8 | Old Town - Balboa Av TC | MTS |
| 851 | 851 | Spring Valley - La Mesa | MTS |
| 704 | 704 | E St Transit Center - Palomar Transit Center | MTS |
| 215 | 215 | Mid-City Rapid | MTS |
| 917 | 917 | Oak Park-Emerald Hills Loop CCW | MTS |
| 963 | 963 | 8th St Transit Center - Paradise Hills | MTS |
| 910 | 910 | Downtown - San Ysidro (OWL Service) | MTS |
| 1 | 1 | Fashion Valley - La Mesa | MTS |
| 6 | 6 | North Park - Fashion Valley | MTS |
| 3 | 3 | UCSD Hospital - Euclid Transit Center | MTS |
| 5 | 5 | Downtown San Diego - Euclid Transit Center | MTS |
| 201 | 201 | Super Loop - Counterclockwise | MTS |
| 227 | 227 | Imperial Beach - Otay Mesa TC | MTS |