From Medivia Online Wiki

Factions are a series of quests and missions that you are asked to complete in support of a certain faction, completing factions can be very fun and rewarding! Kill monsters you wouldn't otherwise attempt, explore places you didn't know existed and be rewarded with valuable items and equipment, gain access to new hunting spots, travel routes and even a new spell for your vocation!

You can work on all factions at once so do not feel like you have to pick one over the other, the main factions are a lot more difficult and time consuming to complete compared to the sub factions.  

Main Factions
thaiansoldier The Imperial Faction
lightbringerknight The Lightbringer Faction
necromantica Order of the Holy Rose
Archini The Archini Faction
Jakob The Grim Faction
Priest of Light.png The White Light Faction
Demon Head.png The Demonic Faction
Sub Factions
RTENOTITLE The Minotaur Faction
dwarfrenegade The Dwarf Faction
elfguardian The Elf Faction
orcwarlord The Orc Faction
slaveguard The Osaris Faction
Djinn Factions*
Marid Marid Faction
Efreet Efreet Faction
*You can choose only one Djinn Faction.