The producers have confirmed in several of their season three podcasts that there are indeed two groups of Others, and that who is on each side will become very apparent in the next couple of episodes. They also jokingly said that there were nine factions of others.

This becomes somewhat apparent in the episode "The Man Behind the Curtain.'' Although this isn't entirely confirmed, this is my educated guess on what the two factions are. Okay (if you haven't seen "The Man Behind the Curtain" you probably don't want to read this), in "The Man Behind the Curtain" we learn that Ben was brought to the island at a young age and that he met a young Richard Alpert (a genuine original inhabitant of the island, a "hostile") who gives him hope of betraying, or not living with Dharma forever. Flash forward ten or so years, and the purge happens, certain members of Dharma felt that they had to join with the original inhabitants of the island for their own survival. Hence, the purge, they gased all of the members, and Dharma is now, unless there were any unseen survirors, dead. Kelvin Inman was left pushing the button, with no hope of replacement coming, because Dharma was simply dead, although he had no way to see this,

So, getting to the point, the two factions of the Others are the original "hostiles", and those select members of Dharma who joined with them. I propose that the Others we get a glimpse of in "The Other 48 Days", and ". . . And Found" are the original inhabitants, born and raised on the island. That is why they are able to make no tracks, have nothing in their pockets, are creepy, etc, etc. There's also people like Ben, and Juliet, and likely many of the other main others who we have seen who were recruited by Ben. However, I propse that Ethan is a original inhabitant, because this would explain why he was so good at tracking, and could drag Charlie and Claire through the jungle, (he could have had help, but I think words said but Juliet in "One of Us" refute this.) This also could explain his seemingly superhuman strength, he's born on an island where things happen that don't happen anywhere else in the world.

I
have a theory that possibly there could be two different groups of others , but as the show has been going on I kinda doubt it .One reason that got me thinking about it is when Ben was saying that they were the good guys. It kind of sounds like they may have been in a fight against two different groups.I'm beginning to think that there is only one group, because all of the incidents with the Others are linked to one group.

A very possible theory now that we have seem the man in the as of yet discovered hatch through the camera Sayid gets working in The Pearl. We momentarily see the one eyed man before he cuts the live - feed on the camera. He is most possibly part of the original Dharma group as Mr. Eko said they had found a glass eye in the arrow along with the bible containing the film reel. That glass eye presumably belonged to him but why he left it behind is also a mystery.

When Ben was still in the guise of Henry Gale just as he was found out he said he would not tell them any information as 'He is a very power man' which could be referencing this man.

Since there is one man on his own it is possible that there may be more people with him.

UPDATED (different person): When I was listening to a podcast, I caught onto something interesting. The producers mentioned something about how there are different levels of others, like castes in Hinduism. Doesn't the guy in the Dharma video look like he could possibly be Indian? This also reveals that there are many different "groups" of others, but they are all working towards the same goal... whatever that may be.

Also, in "Not in Portland", Jack asks Juliet whether she's going to put him back in his cell. She says "Yes, until they decide what to do with you." She doesn't say, "until Ben decides what to do with you" or "until we decide what to do with you". She says "they", which means that there must be a more important group of Others somewhere, on the Island or not, which is in command. It's not the first time we have been deceived, the last time was when we thought Tom was the head of the others. This may seem like a bit of a stretch, but the stretches seem to come true more often then not, am I wrong?