Tor uses a centralized directory authority system where a set of trusted servers maintain the consensus on relay nodes, their bandwidth, and their capabilities. This centralization provides consistent, high-quality information about the relay network but creates identifiable authority servers that adversaries could target to disrupt the network or gather information about its structure.
I2P uses a fully distributed DHT (Distributed Hash Table) for network discovery. There are no central directory servers; each I2P node discovers other nodes through a gossip protocol and maintains its own distributed routing table. This architecture is theoretically more resistant to centralized disruption but can result in routing quality that varies more than Tor's centrally coordinated approach.
Practical implications: Tor provides more reliable performance for accessing external resources and has a much larger user base (millions vs tens of thousands for I2P). I2P provides better theoretical resistance to certain directory-server-targeting attacks and has a more active internal application ecosystem with native file sharing, email (Bote), and messaging applications built for the I2P environment.