The rice root nematode Hirschmanniella oryzae is the most abundant plant-parasitic nematode in flooded rice fields and is distributed world-wide. Although it is economically less important than sedentary nematodes, it can cause severe yield reductions and economic losses in specific environmental conditions. No transcriptome data for this genus were available until now. We have performed 454 sequencing on a mixed life stages population to gain an insight into nematode–plant interactions and nematode survival strategies. The results of two assembly strategies were combined to reduce the redundancy of the data, generating a final dataset of 21 360 contigs. The data were screened for putative plant cell wall-modifying proteins, which facilitate nematode migration through host roots. A β-mannanase, previously not reported in nematodes, was detected in the dataset. The data were screened for putative effector proteins that may alter the host defence mechanism. Two enzymes, chorismate mutase and isochorismatase, thought to be involved in the salicyclic acid pathway, were identified. Experimental treatments of H. oryzae with artificial seawater showed that late embryogenesis abundant (LEA) proteins and SXP/RAL-2 are induced, suggesting that these proteins are involved in the process of anhydrobiosis. The newly generated data can highlight potential differences between sedentary and migratory nematodes, and will be useful in the further study of host–nematode interactions and the developmental biology of this nematode.