The regulator announced last month that a number of key senior figures were to leave and some departments would be combined. The changes started to take effect yesterday.
The revamp includes the authorisations and supervision divisions being amalgamated with the specialist supervision functions such as financial crime and client assets.
From April there will be two divisions in order to provide clearer distinction between approaches to the regulation of large and smaller firms.
Tracey McDermott will take responsibility for managing the transition and will subsequently lead one of the new divisions.
There will also be a new strategy and competition division led by Christopher Woolard to build on the FCA's competition capabilities and a risk division, for which Richard Sutcliffe will be the acting director.
{desktop}{/desktop}{mobile}{/mobile}
The changes reflected "lessons learned from recent external reviews", the FCA said. The restructure will be fully implemented by April.
Clive Adamson, the FCA's director of supervision and a member of the executive committee and board member, is departing as part of the shake up.
He told MPs that a report criticising the FCA over a botched media briefing, which led to billions of pounds wiped off leading insurers' share values last March, did become a factor in the timing of his exit, though he had already planned to move on.
Fellow executive committee members Zitah McMillan and Victoria Raffe are also leaving the organisation.
Martin Wheatley, chief executive of the FCA, said: "In the 18 months since the inception of the FCA we have achieved a lot, and now is the time to sharpen our focus, to look at how we can deliver our objectives and ambitions to the best of our abilities. The financial industry continually evolves and to regulate it effectively we must evolve too."
A new markets policy and international division led by David Lawton will focus on increasing the FCA's focus and influence on the European stage.   

Get FREE daily news summaries direct to your inbox. Sign up on the homepage now.
Follow us on Twitter  and get frequent news alerts @FPM_online.
Or follow Editor Kevin O'Donnell - @FPM_Kevin or staff writer James Nadal - @FPM_James.
For the latest Sipp, SSAS and retirement news visit our sister news site www.sippsprofessional.co.uk and on Twitter @SippsPro.