Plasmopara halstedii and Plasmopara viticola are the causative agents of downy mildew respectively on sunflower and grapevine, two economically important crops. These phylogenetically related oomycetes are obligate biotrophs belonging to Peronosporales but have different pathological profiles. Despite the economic importance of diseases caused by both Plasmopara, genomic resources are very limited and their effector repertoire is unknown. We performed parallel transcriptome sequencing of Pl. halstedii and Pl. viticola and released a Plasmopara species cDNA database (PlasmoparaSp) containing 46 000 clusters. In oomycetes, two classes of effectors are translocated into the host cytoplasm, the RXLRs and the CRNs. We screened the PlasmoparaSp database in order to identify the repertoire of expressed effectors used by both Plasmopara species, about 50 putative RXLR and 60 CRN were identified for each. We compared these effectors within both species and with seven publicly available oomycete species representative of Peronosporales and Albuginales. Sequence analyses revealed the presence of 55 RXLR families, 12 of them shared by both Plasmopara, and 19 showing amino acid conservation with predicted peptides from at least one oomycete species. Analyses of Plasmopara sp. CRN C-terminal variable regions revealed sequence conservation inside Plasmopara sp. and across oomycetes, excepting H. arabidopsidis. Finally, our analyses confirmed the presence of 8 CRN C-terminal domains described in Phytophthora infestans and identified CRN effectors showing similarity to serine proteases. We report effectors identified as species-specific, which may be involved in host specificity, as well as effectors conserved among oomycetes that might play important roles in the pathogens biology.