Yes, thanks James, my original source was confused. Here's some of the further details:
In 1849 he returned to Göttingen and his Ph.D. thesis, supervised by Gauss, was submitted in 1851. However it was not only Gauss who strongly influenced Riemann at this time. Weber had returned to a chair of physics at Göttingen from Leipzig during the time that Riemann was in Berlin, and Riemann was his assistant for 18 months. Also Listing had been appointed as a professor of physics in Göttingen in 1849. Through Weber and Listing, Riemann gained a strong background in theoretical physics and, from Listing, important ideas in topology which were to influence his ground breaking research.

Riemann's thesis studied the theory of complex variables and, in particular, what we now call Riemann surfaces. It therefore introduced topological methods into complex function theory. The work builds on Cauchy's foundations of the theory of complex variables built up over many years and also on Puiseux's ideas of branch points. However, Riemann's thesis is a strikingly original piece of work which examined geometric properties of analytic functions, conformal mappings and the connectivity of surfaces.

In proving some of the results in his thesis Riemann used a variational principle which he was later to call the Dirichlet Principle since he had learnt it from Dirichlet's lectures in Berlin. The Dirichlet Principle did not originate with Dirichlet, however, as Gauss, Green and Thomson had all made use if it. Riemann's thesis, one of the most remarkable pieces of original work to appear in a doctoral thesis, was examined on 16 December 1851. In his report on the thesis Gauss described Riemann as having:

... a gloriously fertile originality.

On Gauss's recommendation Riemann was appointed to a post in Göttingen and he worked for his Habilitation, the degree which would allow him to become a lecturer. He spent thirty months working on his Habilitation dissertation which was on the representability of functions by trigonometric series. He gave the conditions of a function to have an integral, what we now call the condition of Riemann integrability. In the second part of the dissertation he examined the problem which he described in these words:

While preceding papers have shown that if a function possesses such and such a property, then it can be represented by a Fourier series, we pose the reverse question: if a function can be represented by a trigonometric series, what can one say about its behaviour.

To complete his Habilitation Riemann had to give a lecture. He prepared three lectures, two on electricity and one on geometry. Gauss had to choose one of the three for Riemann to deliver and, against Riemann's expectations, Gauss chose the lecture on geometry. Riemann's lecture Über die Hypothesen welche der Geometrie zu Grunde liegen (On the hypotheses that lie at the foundations of geometry), delivered on 10 June 1854, became a classic of mathematics.
--via Riemann biography http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Riemann.html