Rykodisc had some notable successes in the CD-reissue industry, as artists such as Elvis Costello, David Bowie, Yoko Ono, Frank Zappa, Nine Inch Nails, Robert Wyatt, and Mission of Burma allowed Rykodisc to issue their catalogs on CD. Rykodisc still retains the rights to the Zappa and Mission of Burma catalogs. Rykodisc also re-released the classic SST Records-era recordings by the Meat Puppets.
Over the years the label has acquired Hannibal Records, Tradition Records, Gramavision Records, Emperor Norton Records, and Restless Records, as well as founded a distribution company, Ryko Distribution and a music publishing company, Rykomusic. The label's catalogue now exceeds 1,200 titles.
In 1998, Chris Blackwell left Island Records and bought Rykodisc for a reported $35 million as a means of acquiring music marketing and distribution expertise for his new venture, a media company called Palm Pictures.
In 1999, one year after the Blackwell buy-out, the office in Salem MA was closed, and many industry veterans were laid off. The office held a wake for the label.
In 2001 Blackwell parted ways with Rykodisc. The label was then located in New York with offices in Los Angeles and in Beverly, Massachusetts.
Rykodisc sets apart its CD issues with its trademarked green-tinted jewel boxes, which the company began using in 1988. The label began limiting the use of the green-tinted cases on new releases in 2002.
On March 23, 2006, it was announced that Warner Music Group acquired the Ryko Corporation for $67.5 million. When Warner bought Ryko, it acquired the label's Frank Zappa master tapes, entitling Warner to any reissue rights—an irony considering Zappa's outspoken hatred for the major record label.