At the end of the Orange League season (Episode 118 "The Rivalry Revival"), when Ash talks with Professor Oak and decides to continue travelling to the Johto region, Prof. Oak gives him a new Pokédex. In every new region Ash goes to, he get a new Pokédex to catalogue the new Pokémon living there.
Strangely enough, though, in episode 50 "Who Gets To Keep Togepi", Oak tells Ash there's a new upgrade to the Pokédex, saying "Well, now you can get details on all the latest Pokemon discoveries", and upgrades Ash's Pokédex.
At first it really wasn't clear why Ash should get that upgrade, but later in the same episode this question is cleared up, as Ash gets to see Togepi and says "Hey, now that Dexter is been upgraded he'll know the answer". Although Togepi is from the next generation, the Pokédex now has the info on Togepi (although it does say that more info about its species is still unavailable) rather than saying "there are still Pokémon yet to be identified" like in the first episode with Ho-Oh.
Anyway, this upgrade seems to make the Pokédex know the species in the 2nd Gen, which makes me wonder why Ash needs a new Pokédex for the Johto region since the Pokédex had already been upgraded to know the Johto Pokémon species, and we don't see any great difference in the new Pokédex except its design.
(Although it may need evidence, since the Pokédex clearly says the there's not much data on Togepi, since it's not new the Pokédex might say that like in Ep.23 "The Tower Of Terror" the Pokédex said the same about Gastly, Haunter and Gengar.)