Ultramarines came close to extinction but survived due to the courrage and tenacity of the First Company.
I remember reading a while back that the fleets of Tyranid have devouered some planets that had Space Marine fortress monasteries on them. I taught those were the Silver Skulls and the Howling Gryphones but a Quick Google disproved me. Is there a list of all the Space Marine chapters lost to Kraken/Leviathan??