| Flavobacterium acidurans | Type Strain | ATCC® 27383™ | September 5, 2023 | 3.5 Mb | | |
| Flavobacterium aquatile | Type Strain | ATCC® 11947™ | November 30, 2021 | 3.5 Mb | | |
| Flavobacterium chilense | | ATCC® 35408™ | June 3, 2024 | 5.9 Mb | | |
| Flavobacterium columnare | Type Strain | ATCC® 23463™ | August 31, 2022 | 3.3 Mb | | |
| Flavobacterium columnare | | ATCC® 49512™ | August 31, 2022 | 3.2 Mb | | |
| Flavobacterium covae | Type Strain | ATCC® TSD-246™ | April 5, 2023 | 3.4 Mb | | |
| Flavobacterium davisii | Type Strain | ATCC® TSD-247™ | September 5, 2023 | 3.4 Mb | | |
| Flavobacterium denitrificans | Type Strain | ATCC® BAA-842™ | September 5, 2023 | 4.8 Mb | | |
| Flavobacterium frigidarium | Type Strain | ATCC® 700810™ | September 5, 2023 | 3.7 Mb | | |
| Flavobacterium hibernum | Type Strain | ATCC® 51468™ | September 5, 2023 | 5.4 Mb | | |
| Flavobacterium johnsoniae | Type Strain | ATCC® 17061™ | August 27, 2019 | 6.1 Mb | | |
| Flavobacterium johnsoniae subsp. aurantiacum | Type Strain | ATCC® 23107™ | February 21, 2025 | 5.5 Mb | | |
| Flavobacterium okayamensis | | ATCC® TSD-280™ | December 12, 2022 | 2.8 Mb | | |
| Flavobacterium oreochromis | Type Strain | ATCC® TSD-248™ | September 5, 2023 | 3.5 Mb | | |
| Flavobacterium pectinovorum | Type Strain | ATCC® 19366™ | November 30, 2021 | 5.6 Mb | | |
| Flavobacterium psychrophilum | Type Strain | ATCC® 49418™ | November 30, 2021 | 2.7 Mb | | |
| Flavobacterium psychrophilum | | ATCC® 49511™ | August 27, 2019 | 2.9 Mb | | |
| Flavobacterium saccharophilum | Type Strain | ATCC® 49530™ | August 8, 2023 | 5.2 Mb | | |
| Flavobacterium sp. | | ATCC® 29590™ | October 31, 2023 | 6.2 Mb | | |
| Flavobacterium sp. | Type Strain | ATCC® TSD-440™ | March 24, 2025 | 5.3 Mb | | |
| Flavobacterium tructae | | ATCC® BAA-2541™ | September 5, 2023 | 5.4 Mb | | |