The conservation and sustainable management of rare and heritage seed varieties face critical challenges in ownership verification, provenance tracking, and supply chain transparency. Traditional paper-based certification systems are vulnerable to fraud, data loss, and lack real-time traceability across complex agricultural networks. Non-fungible tokens (NFTs) built on blockchain infrastructure offer unprecedented opportunities for immutable digital certification, transparent ownership transfer, and end-to-end supply chain monitoring of rare seed germplasm. This review examines the technical architecture, implementation strategies, and practical applications of NFT-based systems for rare seed variety management. We analyze tokenization protocols that encode genetic identity, geographic origin, and custodial history into unique digital assets, alongside smart contract mechanisms that automate verification, enforce breeding rights, and facilitate transparent marketplace transactions. Key applications include digital seed passports for heirloom varieties, blockchain-enabled seed bank registries, farmer-to-farmer exchange platforms, and regulatory compliance systems for plant genetic resources. Despite promising pilot deployments demonstrating enhanced traceability and stakeholder trust, significant barriers persist including scalability limitations, energy consumption concerns, interoperability gaps between agricultural databases and blockchain networks, legal ambiguities surrounding digital ownership of biological materials, and limited technical capacity among smallholder farming communities. Future development trajectories emphasize energy-efficient consensus mechanisms, mobile-accessible interfaces, integration with Internet of Things sensor networks for automated data capture, and harmonization of international legal frameworks governing NFT-based seed ownership rights.