Despite both sticking to a carefully worded policy that there is only "one China", Taiwan and China differ over issues including when the country was founded, and also use different Chinese characters. And China made it clear that it still considers Taiwan as less than equal.
When the two sat down for talks it was Xi who spoke first. Ma, a democratic politician used to interacting with the public, held his own relaxed press conference afterward.
But Xi sent a lower-level official to face the media on his behalf. And while Ma left the hotel from its front entrance, pausing to wave to dozens of gathered reporters, Xi apparently exited in secret.
Referring to the handshake at the start of the hour-long, mostly closed-door meeting with Xi, Ma said: "We crossed 66 years of space and time to stretch out our hands and shake them together, holding in our hands the past and future of both sides of the [Taiwan] strait."
"The 66-year history of cross-Strait relations testifies that no matter how great the difficulty, no matter how many risks there are, no force can pull us apart," Xi told Ma.
The meeting comes weeks before elections on the island which are expected to result in victory for Ma's rivals the Democratic Progressive Party - a result Beijing is desperate to avoid given the DPP's traditional stance in favour of independence from China.
"The visuals are important for them," said Michael Cole, a Taiwan expert from the University of Nottingham. "It is a landmark meeting, but in terms of substance there is practically nothing."Telegraph Group Ltd, AFP