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Thirty-two fungal polyketide derivatives, including eleven new compounds, namely (3<i>R</i>,5′<i>R</i>)-5-hydroxytalaroflavone (<b>1</b>), talaroisochromenols A–C (<b>3</b>, <b>5</b>, and <b>11</b>), (8<i>R</i>,9<i>R</i>,10a<i>R</i>)-5-hydroxyaltenuene (<b>13</b>), (8<i>R</i>,9<i>R</i>,10a<i>S</i>)-5-hydroxyaltenuene (<b>14</b>), (8<i>R</i>,9<i>S</i>,10a<i>R</i>)-5-hydroxyaltenuene (<b>15</b>), nemanecins D and E (<b>25</b> and <b>26</b>), 2,5-dimethyl-8-iodochromone (<b>27</b>), and talarofurolactone A (<b>29</b>), together with one new naturally occurring but previously synthesized metabolite, 6-hydroxy-4-methoxycoumarin (<b>28</b>), were isolated and identified from the deep-sea cold-seep-derived fungus <i>Talaromyces</i> sp. CS-258. Among them, racemic ((±)-<b>11</b>) or epimeric (<b>13</b>–<b>15</b>, <b>25</b>, and <b>26</b>) mixtures were successfully separated by chiral or gradient elution HPLC. Meanwhile, compound <b>27</b> represents a rarely reported naturally occurring iodinated compound. Their planar structures as well as absolute configurations were determined by extensive analysis via NMR, MS, single-crystal X-ray diffraction, Mosher’s method, and ECD or NMR calculation (with DP4⁺ probability analysis). Possible biosynthetic routes of some isolated compounds, which are related to chromone or isochromone biosynthetic pathways, were put forward. The biological analysis results revealed that compounds <b>7</b>, <b>9, 10, 18</b>–<b>22</b>, <b>24</b>, <b>30</b>, and <b>31</b> showed broad-spectrum antibacterial activities against several human and aquatic pathogens with MIC ranges of 0.5–64 μg/mL.