Flower shape and colour are key plant traits which are often strongly correlated with pollinator choice and reproductive isolation. To understand the genetic changes underlying variation in these traits, we performed the first QTL analyses of these traits in Streptocarpus (Gesneriaceae) using a segregating backcross (BC) population of (S. rexii × S. grandis) × S. grandis. Composite traits of floral dimensions were dissected into smallest definable subtraits to examine the efficiency of QTL mapping and correlation between composite and subtrait-specific QTLs. Strong dominance effects were observed in the F1 for many S. rexii traits but for few S. grandis traits. In the BC plants new phenotypes appeared that may be the result of transgressive segregation. Many phenotypic correlations were found between floral dimension traits, which was probably due to the co-localisation of QTLs on the linkage groups. Two regions were associated with large numbers of size and shape traits (17 linked on LG1 and eight linked on LG12), to which the first principal component was also mapped. QTLs of composite traits were mostly overlapping with subtraits, although a few QTLs were newly discovered in subtrait mapping. Strong QTLs were detected for time to flowering and for floral pigmentation traits, ventral lobe pigmentation and the yellow spot. The absence of linkage of floral dimension traits and flower pigmentation suggests that genetic regulation of floral form in Streptocarpus allows versatility, perhaps allowing fast response to changing selective pressures from pollinators.