Answer to the question whether convergent novelties share a common genetic basis is vital to understand to what extent that evolution is predictable. Convergent evolution of innovative anal fin pigmentation patterns in cichlid fishes is an ideal model for studying this question. Here, we focused on two patterns: 1) egg-spots, the circular pigmentation pattern in haplochromine lineage with different numbers, sizes and positions; 2) the blotch, with irregular boundary that is independently evolved in the ectodine lineage with limited variation. Based on a thorough comparative transcriptomic and genomic analysis, we found a common genetic basis (i.e. genes related to pigment cells, signaling pathways and metabolic pathways) with accelerated evolutionary rates between the blotch and egg-spots, suggesting that convergent evolution is in parallel with gene expression level, at least for the common genetic basis. In addition, connections of common genes to transcription factors and integration of advantageous genes with accelerated evolutionary rates related to signalling pathways were found for egg-spots gene network. Thus, we propose a hypothesis that re-use of the common genetic basis indicates their important conservative functions (eg. toolkit genes) for the origin of these convergent novel phenotypes, whereas independently evolved connections of common genes to transcription factors and the integration of advantageous genes are important for the emergence and higher evolvability of egg-spots, which is crucial to make it as a key innovation for the adaptive radiation of cichlid fishes. This hypothesis will further illuminate the mechanism of origin and evolution of novelties in a broad sense.