Lake Tanganyikas rocky shoreline is populated by 120 distinct populations of the Cichlid fish species from the genus Tropheus, which represent an ideal system to study evolutionary processes. To gain insight into adaptive morphological changes, pond-breeding experiments with a standardized set-up were carried out starting in 2005. Altogether four ponds were stocked, one containing T. moorii ‘Nakaku, one with T. moorii ‘Mbita and two ponds to produce hybrids in both sex-constellations. To prevent backcrossing, the adult fish were removed after each year, so that three generations of pond-offspring were produced. Fish were allowed to interact, compete and mate freely under standardized rearing conditions. To assess the overall morphology of the pond-bred individuals, fish were anesthetized and scanned with a flatbed scanner to obtain digital images for further analysis. Geometric morphometric methods were used to digitize those images and compare the shape of the fish. In total 583 individuals from two populations and their hybrids over three generations were used for geometric morphometric analysis. Results from Principal Component Analysis of shape variation showed that fish from F2 and F3 were more similar to each other than they were to the F1 fish. Also, as expected, the two cohorts of hybrid progeny obtained from the two sex-constellations of the parents were more similar to each other than to the pure pond-offspring from ‘Mbita and ‘Nakaku. Interestingly, the deformation grid analysis showed that most morphological variation occurred in the head region, suggestive of trophic adaptation. Our results suggest that head morphology in T. moorii morphs is a phenotypically plastic trait that can facilitate rapid adaptation to environmental change. Based on our results we postulate that to the ability for extremely rapid morphological change in ecologically relevant traits might have contributed to the spectacular adaptive radiation of East African cichlids.