Successful growth and development of the posthatching blastocyst and pregnancy establishment are a result of the interaction between a competent embryo and a receptive uterine environment. We examined the global transcriptome profiles of the Day 16 bovine conceptus and pregnant endometrium tissues using RNA-Seq to identify genes that contribute to the dialogue during the period of pregnancy recognition. Using stringent filtering criterion, a total of 16 018 and 16 262 transcripts of conceptus and pregnant endometrium origin, respectively, were identified with distinct tissue-specific expression profiles. Of these, 2261 and 2505 transcripts were conceptus and endometrium specific. Using Cytoscape software, a total of 133 conceptus ligands that interact with corresponding receptors on the endometrium and 121 endometrium ligands that interact with corresponding receptors on the conceptus were identified. While 87 ligands were commonly detected, 46 were conceptus specific and 34 endometrium specific. This study is one of the first to provide a comprehensive list of potentially secreted molecules in the conceptus that interact with receptors on the endometrium and vice versa during the critical window of maternal recognition of pregnancy. The identified tissue-specific genes may serve as candidates to study pregnancy recognition and they or downstream products may represent potential early markers of pregnancy.