Coconut (Cocos nucifera L.), which belongs to family Arecaceae, is an important economic crop of the tropics. Despite its economic significance, applications of genomics science in the coconut crop improvement programs has gained momentum only in recent times. Besides the whole genome and transcriptome sequencing approaches, genomics of plastids and mitochondria of coconut are worthwhile objects of examination for delineating the molecular evolutionary genomics of lands plants in general and palms in particular. Plant mitochondria and chloroplasts have semi-autonomous genetic systems. The genome sequences of both the mitochondria and chloroplast of coconut were made publicly available prior to the sequencing of its nuclear genome. In this chapter, we present the comprehensive structural and functional organization of organellar genomes of coconut. Also, the outcomes of the molecular phylogeny and comparative genomics of chloroplast and mitochondria among the monocots are discussed.