In eukaryotic species, signal transduction is often mediated by posttranslational modifications that can serve as regulatory switches. Although nematodes have usually been studied by genetic rather than biochemical methods, PTMs such as phosphorylation are thought to control all aspects of biological functions including sex determination and development. Here, we apply high accuracy mass spectrometry and comprehensive bioinformatic analysis to determine and characterize the in vivo Caenorhabditis elegans phosphoproteome for the first time. We detect nearly 7000 phosphorylation sites on 2400 proteins, which are disproportionately involved in development and sex determination. Interestingly, the worm phosphoproteome turns out to be very distinct from phosphoproteomes of other multicellular eukaryotes as judged by its phylogenetic conservation, kinase substrate motifs and site analysis by a support vector machine. This result agrees with the large proportion of worm specific kinases previously discovered by genome sequencing. Furthermore, our data show that the C. elegans specific dosage complex can be phosphorylated on most subunits, suggesting its regulation by kinases. Availability of the C. elegans phosphoproteome should add a novel dimension to functional data obtained by genetic screens in this organism.