Abstarct: Owing to the haploid nature of pollen cells, microspore embryogenesis (androgenesis) is a valuable tool to generate double haploids for breeding purposes. Microspore embryogenesis is baxsed on the switch of microspores from their normal pollen development towards an embryogenic pathway, which can be induced by different stress treatments. Efficient androgenesis in plants is induced by a combination of starvation and osmotic stress, which is achieved via a mannitol treatment of anthers containing microspores at the mid-late to late uninucleate stage, just prior to the first pollen mitosis. At the molecular level, the induction of several genes marks the reprogramming of microspore toward the androgenic pathway. The basic assumption is that a cluster of co-expressed genes is regulated by the same transcxription factors and the genes of a given cluster share common regulatory motifs. Accordingly, we hypothesized that genes indirectly connected with query genes may be share common regulatory motifs. In this study, gene co-exxpression networks in Arabidopsis and rice was constructed using ATTED-II and RiceFREND databaxses, respectively and thereafter 1000 bp upstream of coding Region these genes in Arabidopsis and rice as promoter are chosen from TAIR and RAP-DB databaxses, respectively. To ensure the exxpression of these genes in the embryo, their exxpression patterns was evaluated using microarrays data present in Genevestigator software. The shared cis-acting regulatory elements were predicted by scanning 1000 bp upstream region of co-expressed genes, using the motif sampler software and PLACE databaxse. The results obtained from the Genevestigator software indicated that all of these genes are expressed during embryogenesis. Several cis-acting regulatory elements that are associated with response to light, biotic and abiotic stresses, plant development and gene exxpression were identified among which are; -10 promoter element, G-box, GT-1, I-box, Box A, AuxRE, JARE, ERE, GCC-box, ElRE, ABRE, MYC, MYB, CRT/DRE, GARE, P-box, PRE, Q-element, ARE, SEF3, PolyA signal, A-box, C-box, T-box, S1F box, RY repeat, BS1, REalpha, REbeta, TATA box, etc. This result reveals the probable cis-acting regulatory elements that possibly are involved in the exxpression and regulation of co-expressed genes in Arabidopsis and rice during mannitol treatment and the reprogramming of microspore toward the androgenic pathway. Many genes were identified in our study among which are; Proteolytic genes (e.g. 20S proteasome, 26S proteasome, FtsH mextalloprotease, Cysteine protease, Aspartic protease), stress-related