The extinction of the Passenger Pigeon had two major causes: commercial exploitation of pigeon meat on a massive scale and loss of habitat.

Large flocks and communal breeding made the species highly vulnerable to hunting. As the flocks dwindled in size, populations decreased below the threshold necessary to propagate the species. Naturalist Paul R. Ehrlich wrote that its extinction "illustrates a very important principle of conservation biology: it is not always necessary to kill the last pair of a species to force it to extinction."

Another significant reason for its extinction was deforestation. The birds traveled and reproduced in prodigious numbers, satiating predators before any substantial negative impact was made in the bird's habitat. It is unclear the extent to which deforestation impacted important habitats for the species, since large swaths of forested area continued to be present throughout the habitat of the Passenger Pigeon well into the latter half of the 19th century.

In 1857, a bill was brought forth to the Ohio State Legislature seeking protection for the Passenger Pigeon. A Select Committee of the Senate filed a report stating, "The passenger pigeon needs no protection. Wonderfully prolific, having the vast forests of the North as its breeding grounds, traveling hundreds of miles in search of food, it is here today and elsewhere tomorrow, and no ordinary destruction can lessen them, or be missed from the myriads that are yearly produced." 

Conservationists were ineffective in stopping the slaughter. A bill was passed in the Michigan legislature making it illegal to net pigeons within two miles (3 km) of a nesting area, but the law was weakly enforced. By the mid-1890s, the Passenger Pigeon almost completely disappeared. In 1897, a bill was introduced in the Michigan legislature asking for a 10-year closed season on Passenger Pigeons. This was a futile gesture. Similar legal measures were passed and disregarded in Pennsylvania. This was a highly gregarious species  – the flock could initiate courtship and reproduction only when they were gathered in large numbers; smaller groups of Passenger Pigeons could not breed successfully, and the surviving numbers proved too few to re-establish the species. Attempts at breeding among the captive population also failed for the same reasons. The Passenger Pigeon was a colonial and gregarious bird practicing communal roosting and communal breeding and needed large numbers for optimum breeding conditions.

By the turn of the 20th century, the last known group of Passenger Pigeons was kept by Professor Charles Otis Whitman at the University of Chicago.  Whitman studied these pigeons along with Rock Doves and Eurasian Collared-Doves. All of Whitman's pigeons were descended from the same pair. Whitman and the Cincinnati Zoo attempted to breed the surviving birds, including attempts at making a Rock Dove foster Passenger Pigeon eggs. Whitman sent a female named Martha to the Cincinnati Zoo in 1902. While Whitman had about a dozen Passenger Pigeons in 1903, they had stopped breeding, and by 1906 he was down to five birds.

On September 1, 1914, Martha, the last known Passenger Pigeon, died in the Cincinnati Zoo. Her body was frozen into a block of ice and sent to the Smithsonian Institution, where it was skinned, dissected, photographed and mounted. Currently, Martha is in the museum's archived collection and not on display. A memorial statue of Martha stands on the grounds of the Cincinnati Zoo.