Though biological and artificial complex systems having inhibitory connections exhibit high degree of clustering in their interaction pattern, the evolutionary origin of clustering in such systems remains a challenging problem. Using genetic algorithm we demonstrate that inhibition is required in the evolution of clique structure from primary random architecture, in which the fitness function is assigned based on the largest eigenvalue. Further, the distribution of triads over nodes of the network evolved from mixed connections reveals a negative correlation with its degree providing insight into origin of this trend observed in real networks. PACS numbers: 89.75.Fb,02.10.Yn,89.75.Hc,87.23.Kg Structural features of interaction patterns in complex systems are not completely random, they possess some non-random part, possibly dynamical response dependent local or global structures [1]. Several models as well as statistical measures have been proposed to quantify specific features of networks like degree distribution, small world property, community structure, assortative or disassortative mixing etc. Abundance of cliques of order three, indicated by high clustering coefficient (C), plays a crucial role in organizing local motif structures that enhance the robustness of the underlying system [9,10] are rich in the clique structure. Moreover, the local C of nodes have been found to be negatively correlated with their degree in metabolic networks [4]. This paper presents a novel method to understand the evolution of clustering and distribution pattern of cliques over nodes which are known to lead hierarchical organization of modularity in network. Here we use stability criteria for genetic algorithm to choose from the population which leads to the evolution of clustering in the final network. We find that presence of inhibitory links during evolution is very crucial for evolution of clustering.Previous attempts to provide evolutionary understanding of emergence of cooperation [11] as well as to use clustering based constraints for the evolution of other structural properties [12] fail to incorporate effect of inhibition in the connection. Coexistence of inhibitory and excitatory couplings have been implicated in various systems. For instance, in ecosystems, competitive, predatorprey and mutualistic interactions exist among communities of species [13]. Excitatory (friendly) and inhibitory (antagonistic) interactions are also evident in social systems [14]. In neural networks, excitatory and inhibitory synapses regulate the potential variations in neural populations [15]. In context of ecological systems, a celebrated * sarika@iiti.ac.in work by Robert May demonstrates that largest real part of eigenvalues (R max ) of corresponding adjacency matrix, determined by equal contribution from connectivity and disorder in coupling strength contains information about stability of the underlying system [13]. Spectral properties for matrices of ecological and metabolic systems have been further shown to be useful for determi...