there is a related concept called the silurian hypothesis and several tv shows, movies and books have been written around this subject, including they live, V, the works of robert e. howard.
as expressed in conspiracy circles there is something called the cryptoterrestrial hypothesis - which deals with the concept that ufos are more likely to be of earthly origins and part of a separate hidden advanced race of beings or maybe races of beings which are limited in number and make a big show every few thousand years to scare humans into a type of truce or partnership, there is fiction that deals with this going back to the 1800s.
the upper crust of the earth is quite thick (~60miles) and relatively unexplored, it would be possible to build stable habitats under the ocean's bottom and they would be relatively hidden.
now how do you go about testing this theory? well you could scan every single person at birth give them some type of cryptographically secure bio marker so in about 100 years when all the non chipped humans are dead it will be very difficult for the non-humans masquerading as humans to operate in a society where every detected/birthed human is accounted for.
given the improbability of something like that happening and the likely scenario that there might be less than 5000 'aliens' hiding among the surface humans it seems highly unlikely that any means of exposing them would succeed. it would be like looking for vampires, unlikely there are any, but how would you know?
