In order to prevent one man from gaining as much power as Horus had, the branches of the Imperial armed forces were separated, the Inquisition was founded, and the loyal Space Marine Legions were divided into Chapters of roughly one thousand Marines, in accordance with the Codex Astartes.
The Second Founding was not universally accepted; the Space Wolves and Imperial Fists, in particular, objected to dividing their Legions, and the Imperium was nearly torn apart by another civil war. For better or for worse, Leman Russ and Rogal Dorn finally relented, although the Black Templars have since grown their numbers to many more times the usual size - which is perfectly legal, since the Codex and the law allow "crusading chapters" to ignore the limitations due to the expectation of constant fatalities needing replacement. One must wonder how much less grimdark Warhammer 40K would be if the chapters all realized that they are all technically crusading, and even if they weren't, the Great Crusade never officially ended, therefore...yeah. Although that would very quickly turn every little Astartes secession party, like the Badab War, into another Horus Heresy.
List of Second Founding Chapters
- Angels of Absolution
- Angels of Redemption
- Angels of Vengeance
- Lions Sable (They were destroyed trying to apprehend several Fallen in what was later revealed to be a massive trap set by Cypher shortly before The Beheading and all records of their existence were erased to hide the involvement of the Fallen in their collapse.)
- Star Phantoms - (maybe, though this chapter definitely did exist in M31)
- Angels of Vigilance - (Again, maybe, though this one is more likely)
According to The Unforgiven by Gav Thorpe, the Angels didn't get started with their Inner Circle and Fallen Hunting until some decades after the Second Founding so it may be possible that some of the Dark Angels Second Founding chapters are exempted from this practice and hierarchy. Though since all twelve chapters were present at Cypher's revelation and that the majority of officers would have been veterans of the Horus Heresy and the Scouring, it's more likely that Unforgiven would been of one mind and joined willingly and any dissenting voices silenced or sworn to absolute secrecy. While much of the truth is lost to apocrypha and LIES, it does explain the Star Phantoms at least.
- Black Templars
- Crimson Fists
- Soul Drinkers (sort of, it's a long story)
- Fists Exemplar (Mostly destroyed by The Beast. The survivors were absorbed into the Imperial Fists, or defected to the Iron Warriors)
- Iron Knights
The Apocrypha of Skaros indicates that the Ultramarines sired 23 chapters, but doesn't name them all. The listed second founding chapters are given below:
- Aurora Chapter
- Black Consuls
- Desert Lions
- Doom Eagles
- Eagle Warriors
- Genesis Chapter
- Iron Snakes
- Patriarchs of Ulixis
- Praetors of Orpheus
- Silver Eagles
- Silver Skulls
- White Consuls
- Yellow Jackets
The rest of the second founding Ultramarines have been added piecemeal as time goes by.
Also note that the Ultramarines "adopted" some of the loyalist forces from otherwise traitorous legions and permitted them to call themselves Ultramarine Second Founding chapters.
The Scythes of the Emperor were the Ultramarines 199th Company on Sotha, who became the Ultramarines eleventh company as part of the second founding. But were eventually rolled into their own chapter during the Third Founding.
None, as there weren't enough Salamanders left after the Horus Heresy to fill one Chapter, let alone two.
The Grey Knights were not created from any of the Space Marine Legions, as their gene-seed was specially created by the God-Emperor of Mankind himself and their founding members were hand-picked by Malcador the Sigillite; many of them were loyalists who had formerly been a part of a Traitor Legion (e.g. Nathaniel Garro, Garviel Loken, and Iacton Qruze). They were founded to supply the newly-formed Inquisition with a strike force against future Chaos threats.
Some chapters have histories which stretch back to the Second Founding, but who have deliberately obfuscated their parent legion for one reason or another.