Blakiston explored western Canada with the Palliser Expedition between 1857 and 1859. Mount Blakiston, the highest point in Waterton Lakes National Park was named for him in 1858. In 1861, he traveled up the Yangtze River in China, going further than any Westerner before him. He spent the next part of his life in Japan and became one of the major naturalists in that country. Blakiston was the first person to notice that animals in Hokkaidō, Japan's northern island, were related to northern Asian species, whereas those on Honshū to the south were related to those from southern Asia. The Tsugaru Strait between the two islands was therefore established as a zoogeographical boundary, and became known as "Blakiston's Line". Blakiston collected an owl specimen in Hakodate, Japan in 1883. This was later described by Henry Seebohm and named Blakiston's fish owl.
Blakiston married Ann Mary Dun in 1885. She was the daughter of James Dun and the sister of Edwin Dun. They had one daughter and one son. Ann Mary survived him by 46 years and died in England in March 1937.
