With the interest in Semantic Web applications rising rapidly, the Resource Description Framework (RDF) and its accompanying vocabulary description language, RDF Schema (RDFS), have become one of the most widely used data models for representing and integrating structured information in the Web. With the vast amount of available RDF data sources on the Web increasing rapidly, there is an urgent need for RDF data management. In this work, we focus on distributed RDF data management in peer-to-peer (P2P) networks. More specifically, we present results that advance the state-of-the-art in the research area of distributed RDF query processing and reasoning in P2P networks. We fully design and implement a P2P system, called Atlas, for the distributed query processing and reasoning of RDF and RDFS data. Atlas is built on top of distributed hash tables (DHTs), a commonly-used case of P2P networks. Initially, we study RDFS reasoning algorithms on top of DHTs. We design and develop distributed forward and backward chaining algorithms, as well as an algorithm which works in a bottom-up fashion using the magic sets transformation technique. We study theoretically the correctness of our reasoning algorithms and prove that they are sound and complete. We also provide a comparative study of our algorithms both analytically and experimentally. In the experimental part of our study, we obtain measurements in the realistic large-scale distributed environment of PlanetLab as well as in the more controlled environment of a local cluster. Moreover, we propose algorithms for SPARQL query processing and optimization over RDF(S) databases stored on top of distributed hash tables. We fully implement and evaluate a DHT-based optimizer. The goal of the optimizer is to minimize the time for answering a query as well as the bandwidth consumed during the query evaluation. The optimization algorithms use selectivity estimates to determine the chosen query plan. Our algorithms and techniques have been extensively evaluated in a local cluster.