The soilborne filamentous fungus Fusarium oxysporum causes devastating diseases of many cultivated plant species. F. oxysporum f. sp. raphani and f. sp. rapae are two of four formae speciales that are pathogenic to Brassicaceae plants. Here, we present high-quality genome sequences of F. oxysporum f. sp. raphani strain Tf1262 and F. oxysporum f. sp. rapae strain Tf1208 that were isolated from radish (Raphanus sativus) and turnip (Brassica rapa var. rapa), respectively. These genome resources should facilitate in-depth investigation of interactions between F. oxysporum and Brassicaceae plants, and enable comparative genomics of the F. oxysporum species complex to uncover how pathogenicity evolved within F. oxysporum.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.