Bacteria wilt (BW) of Casuarina equisetifolia L. Johnson, caused by Ralstonia solanacearum (E. F. Smith) Yabuuchi, is one of the most important diseases of C. equisetifolia L. Johnson, the main coastal protective forest tree in southeast China. The resistance of 33 C. equisetifolia L. Johnson clones to BW was determined by means of hydroponic and pot inoculation methods with the suspension of R solanacearum (E. F. Smith) Yabuuchi as inocula in the two-step procedure. The results showed that clones FJ11 and FJ13 were highly resistant to BW with the lowest disease incidences of 10.8 and 15.8%, respectively, whereas clones FJ9 and GD15 were the most susceptible ones with the highest disease incidences of 100.0%. The analysis of AFLP markers was performed on clones FJ11, FJ13, FJ9 and GD15, and the results indicated that three DNA fragments E-AAA/M-CCG, E-AAG/M-CGC and E-AGG/M-CAA were found to be linked to the BW resistance. BLAST searches revealed that the first two fragments (GenBank accession numbers: KC111411 and KC135871) had no identities to any sequences, and the third one showed a high similarity to some sequences which code for heat shock protein. Taken together, the two resistant clones screened in our research were undoubtedly the valuable resistant resources of C. equisetifolia L. Johnson, and the three AFLP markers could be used in marker-assisted selection of C. equisetifolia L. Johnson in the future.