Plasmopara halstedii and Plasmopara viticola are the causative agents of downy mildew of two economically important crops, sunflower and grapevine, respectively. 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. In this study parallel transcriptome sequencing of P. halstedii and P. viticola was performed, and a Plasmopara species cDNA database (PlasmoparaSp) released containing 46 000 clusters. In oomycetes, two classes of effectors are translocated into the host cytoplasm, the RXLRs and the CRNs. The PlasmoparaSp database was screened 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. These effectors were compared 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 spp. CRN C-terminal variable regions revealed sequence conservation inside Plasmopara spp. and across oomycetes, with the exception of Hyaloperonospora arabidopsidis. Finally, the analyses confirmed the presence of eight CRN C-terminal domains described in Phytophthora infestans and identified CRN effectors showing similarity to serine proteases. Species-specific effectors were identified that may be involved in host specificity, as well as effectors conserved among oomycetes that might play important roles in the pathogen biology.