The　second　near-infrared　(NIR-II)　window,　with　a　broadband　absorption　ranging　from　1000　nm　to　1350　nm,　has　received　increasing　attention　for　photoacoustic　imaging　and　imaging-guided　NIR-II　photothermal　therapy.　Compared　to　conventional　nanoagents　in　the　first　near-infrared　(NIR-I)　window,　with　an　optical　absorption　of　700-1000　nm,　NIR-II　nanoagents　offer　various　merits　such　as　high-performance　photothermal　treatment　outcomes　and　photoacoustic　imaging　with　both　deeper　tissue　penetration　and　higher　SNR.　Thus,　this　review　focuses　on　the　recent　progress　in　photoacoustic　imaging　and　photothermal　therapy　in　the　NIR-II　window.　The　merits　of　the　NIR-II　window　relative　to　the　NIR-I　window　are　systematically　compared.　This　is　followed　by　a　summary　of　nanoagents　in　the　NIR-II　window　and　their　biomedical　application,　including　photoacoustic　imaging　in　the　NIR-II　window　and　imaging-guided　NIR-II　photothermal　therapy.　Finally,　the　prospects　and　challenges　of　both　photoacoustic　imaging　and　photothermal　therapy　in　the　NIR-II　window　are　summarized.　©　2019　The　Royal　Society　of　Chemistry　and　the　Centre　National　de　la　Recherche　Scientifique.