Many people interpreted this as a paean to marijuana, which is also known as "Mary Jane." They were probably right. The song was produced by Bones Howe, who would later work on most of the hits for the 5th Dimension. Howe spoke with Bruce Pollock for the book By the Time We Got to Woodstock: The Great Rock 'n' Roll Revolution of 1969. Writes Pollock: Breaking in with the pot-coded ode "Along Comes Mary," the Association had a long and troubled association with drugs a lot harder than Mary Jane. Bass player Brian Cole overdosed on heroin in 1972. "In the 60s drugs were everywhere," Bones said. "As a producer you had to find ways of getting around that. You'd work in the daytime not at night. If you're working with singers you don't let them have a whole day to laugh and carry on and have a good time and then come in the studio and try to sing. You try to get them at two in the afternoon when they've just gotten up. Most of the time I worked with studio musicians - guys I worked with all the time. I loved what they did and that's why I hired them over and over again and I loved the results we got. I worked with lead sheets, chord sheets, never written arrangements. I made jazz records in the 50s and that was improvised. In the 60s I was improvising with the rhythm section and when I got to the vocal parts we worked out arrangements."
This song was written by Tandyn Almer, who had some success as a songwriter in the '60s and '70s, and was one of the few people that was close friends with Brian Wilson in the early '70s. Tandyn co-wrote the Beach Boys song "Sail On Sailor."
This was the first hit for The Association, who gained a following in Los Angeles, but had a hard time getting a record deal. They signed to a small label called Valiant Records, who were rewarded when this became a hit, and when their follow-up, "Cherish," went to #1.
The Bloodhound Gang covered this on their album Hooray for Boobies. (thanks, James - Tacoma, WA)