The accumulation of maternal mRNA and protein during oogenesis for supporting oocyte maturation and the newly fertilised zygote marks the beginning of developmental process in mammals. MicroRNAs (approximately 18-22 nt long) which are known for post-transcriptional gene regulation are evidenced for their essential role during animal development. We, therefore, aimed to investigate the expression of miRNAs in immature and in vitro matured bovine oocytes, using heterologous miRNA array platform. To attain this, we used a mercury locked nucleic acids (LNA) array (Exiqon, Vedbaek, Denmark) microarray that consist of 454 capture probes for human, mouse and rat miRNAs as registered and annotated in the miRBase release 8.0 at The Wellcome Trust Sanger Institute. Our result revealed the differential expression of 59 miRNAs, of which 31 and 28 miRNAs were found to be preferentially expressed in immature and matured oocytes, respectively. Here, we also report the identification of 32 orthologous miRNAs using a heterologous approach. Expression profiling of selected miRNAs during preimplantation stage embryos showed a distinct temporal expression pattern. After target prediction for selected candidate miRNAs high ranking target mRNA were quantified in immature and matured oocytes and showed a reciprocal expression pattern between the miRNA and the predicted targets suggesting a cause and effect relationship.