Completing your Pokédex is definitely time-consuming especially as you'll have to come across certain rare Pokémon that have very low encounter rates. Some can only be encountered upon meeting certain conditions and specific spot across the entire Alola Region. Here's the list for the Top 5 Rarest Alolan Pokémon in Pokémon Sun and Moon.
Dhelmise
This new Pokémon can be extremely difficult to find if you don't know where to search for it. Dhelmise can only be found in one location and that is in Seafolk Village. Now, even if you know where to fish for the Pokémon, there's only a 1% chance of encountering it unless you're fishing on a bubbling spot - in which the chances of encountering the Pokémon increases to 10%. But even so, it would still take you a couple of minutes if not hours of encountering one.
Castform
Castform is an interesting Pokémon as it can change its form depending on the type of the battlefield it is in. The Pokémon can transform into its Fire, Water or Ice form if subjected to any of the corresponding weather: Sun, Rain or Hail. As unique as it sounds, Castform is one of the toughest Pokémon to catch as it can only be encountered in certain places under certain weather condition. The Pokémon can be called via SOS battle in these specific places: Route 17, Exeggutor Island, Haina Desert, Lush Jungle, Malie Garden and Tapu Village.
Mareanie
Toxapex is considered as one of the strongest Pokémon (non-UB, non-legendary) in Pokémon Sun and Moon. And it evolves from Mareanie, a very rare Pokémon that can only be found via SOS battle of another rare Pokémon, the Corsola, through fishing. Now, finding a Corsola is already a time-consuming process on its own as it only has a 1% encounter rate. But there's a trick, however, that involves fishing on bubbling spots as it theoretically, increases your chances of encountering rare Pokémon by 20%. To take you to the entire process, we've compiled a full guide on how to easily catch a Mareanie.
Salazzle
Salazzle is a brand new Fire/Poison type Pokémon that evolves from Salandit. This Pokémon is very rare because Salandit only evolves into Salazzle if it's female - one of the few Pokémon that need a specific gender in order to evolve. Now, finding Salandit is easy but encountering a female Salandit would take you hours as it only has a 12% encounter rate.
Salamence
Catching Salamence early in the game is definitely something to brag about but this Pokémon, in reality, is painstakingly hard to get. First off, you'd have to go to a specific spot in Route 3 in Melemele Island. After you cross the bridge, you'd come across a patch of grass and here's where your ordeal will begin as you'll have to find a Bagon here that only has a 1% encounter rate. Once you've successfully found a Bagon, do the SOS chaining method until he calls Salamence for help - which also has a 1% encounter rate meaning it would take you literally several hours before you'd ever catch a Salamence via this process.
