Varieties of valuable compounds like- cosmetics are extracted from various animals. Many companies have catered to this expanding market of cosmetics by introducing various makeup types for which they use vibrant colors that are derived from some unexpected sources, ranging from crusted insects to rust, which is responsible for diminution of biodiversity. Therefore there is a strong need to look for alternative source for these compounds (Bioprospecting). In this paper, a bioinformatics approach has been used to analyze the molecular evolution of known valuable compounds like anthraquinone by analysis of pathway and construction of phylogenetic trees. Phylogenetic analysis provides new horizons for this type of study and shows their worthwhile by giving the answers of their origin, development and other characteristics. The phylogenetic analysis of enzymes was incorporated to know, which species are related and which one is the ancestral species. Bioinformatics database, tools and software which were used in the paper are NCBI, KEGG, BLAST, MULTALIN, PHYLIP.After tracing phylogeny of enzymes involved in anthracene degradation pathway,both the enzymes showed ancestral relationship with Oriya sativa. Therefore Oryza sativa can be an alternative source to obtain anthraquinone of plant origin. when phylogenetic relationship for octaketide synthase was traced it showed relationship with pentaketide synthase of Aloe arborescens and chalcone synthase of Naringenin, Hypericum hookerianum, Vitis vinifera and Senna alata and also with aromatic polyketide synthase of Solenostemon scutellarioides. Therefore they can be alternate source to obtain anthraquinones. A list of valuable secondary metabolites and their possible alternative sources is also discussed in the paper.