The head of the city’s special education division has announced that she is stepping down at the end of the school year, a surprise move that comes at a time when a top-to-bottom review of special education is underway.

Linda Wernikoff said her decision to retire is not related to the review or the changes its conclusion could bring to her department. “I think I’ve had a wonderful 35-year career here and I’m very proud of the work that we’ve done,” she told me. “Now I think it’s time that I need to try new things.”

Under Wernikoff’s leadership, the Department of Education has focused on reducing the proportion of children who are in special education-only classes, and the graduation rate for students with special needs has inched up, although it still remains quite low. Wernikoff, who began her career in 1974 as a speech teacher, told me she had no specific plans yet for her future, but she said, “Whatever I do will continue to be advocating for students with special needs.”

People that I spoke to today said Wernikoff’s departure will be a blow for the special education community.

“Linda has formed relationships with many in the advocacy community over the years,” said Kim Sweet, executive director of Advocates for Children of New York (and my former boss). “It will be a major change.”

“Whether you like her or you don’t like her is immaterial but what she has is teaching experience and institutional memory, and when you lose the institution’s memory, you may be condemned to repeat your mistakes,” said Ellen McHugh, a parent who sits on the Citywide Council on Special Education. “It’s sad to see her go.””She has a great understanding of the system,” said Carmen Alvarez, the teachers union’s special education head. “She can connect the dots between all of the programs, and once she goes there’s not going to be anybody else to do that.”

According to Wernikoff and others in the department, there are no specific plans yet about who will take over her role. David Cantor, a DOE spokesman, said Garth Harries, the former McKinsey consultant who is currently leading the special education review, is not under consideration for the spot. When Harries began the review, some questioned whether he had the experience to make decisions about special education.

“Replacing someone with her depth of experience is going to be very difficult,” McHugh said.

Wernikoff has been the top special education official since early 2003, when her predecessor left as part of a shakeup of high-level administration that happened when Joel Klein became chancellor. Klein called Wernikoff’s tenure at the DOE “long and impressive” in a statement he released this afternoon. “Linda has been an outstanding leader in our school system and is enormously respected by parents and educators,” he said. “We will miss her.”