By Miguel Angel Gutierrez

MEXICO CITY (Reuters) - Archeologists have found a mass grave in Mexico City with four dozen human skeletons laid out in neat lines that could reveal clues about the 16th century Spanish conquest that killed millions.

The investigators found the 49 skeletons, all lying face up with their arms crossed, as they searched for a palace complex in the Tlatelolco area, once a major religious and political center for the ancient Aztec elite and now a district in the north of the sprawling Mexican capital.

"We were completely taken by surprise. We didn't expect to find this massive funeral complex," Salvador Guilliem, in charge of the site for the government's archeology institute, said when the discovery was announced on Tuesday.

Historians think the Aztecs built Tlatelolco in the early 1300s along with the nearby city of Tenochtitlan, the capital of the Aztec empire and now the heart of Mexico City, which the Spanish founded after they conquered the Aztecs in 1521.

It is likely the indigenous people buried in the grave died in battle against the invading Spanish or fell victim to diseases that wiped out large swaths of the native population in 1545 and 1576, Guilliem said.

Many Aztec fighters died resisting the Spanish invasion and millions also perished during a four-year epidemic of hemorrhagic fever that began in 1545, killing 80 percent of indigenous Mexicans.

The 13-by-32-foot (four-by-10-meter) burial site differs from other conquest-era graves because of the reverential way the bodies were buried, following Christian customs of the time, unlike thousands of contemporary graves at other Aztec cities where bodies were thrown in at random.

"It is a mass grave, but they were very carefully buried," Guilliem said.

The burials were likely ordered by Spanish overlords but carried out by Aztecs since most of the artifacts found around the bodies, such as copper necklaces and bone buttons, are from pre-Hispanic cultures, he said.

The skeletons of two children, a teenager, and an old person wearing a ring that could signify higher status, were found along with 45 young adults in the tomb.

The scientists expect to find at least 50 more bodies as excavations continue at the massive Tlatelolco complex, home to 67 ancient structures, including massive pyramids.

"The discovery is filling us with more questions than answers at this point," Guilliem said.

(Writing by Mica Rosenberg; Editing by Eric Walsh)