Experiments were conducted in irrigation runoff containment basins to assess the effects of bait species (Camellia japonica, Ilex crenata or Rhododendron catawbiense), bait type (whole leaf vs. leaf disc), baiting duration (1, 2, 7 or 14 days), baiting depth and growth media (modified PARP-V8 or PARPH-V8) on the recovery of Phytophthora species. A two-rope, flexible bait-deployment system was compared with a one-rope fixed system for bait stability at designated locations and depths. A total of 907 Phytophthora isolates were subjected to PCR-based single-strand conformation polymorphism (PCR-SSCP) analysis to identify to species level. Seven distinct SSCP patterns representing six morphospecies: P. citricola (Cil I), P. citrophthora (Cip I), P. hydropathica (Hyd), P. insolita (Ins), P. megasperma (Meg I & II) and an unidentified Phytophthora species were identified. Irrespective of culture medium, 7 days of baiting with rhododendron leaves consistently resulted in the recovery of the greatest diversity and populations of Phytophthora species with minimum interference from Pythium species. The flexible bait-deployment system was superior to the fixed system, minimizing the risk of bait loss and dislocation of baiting units and allowing baits to remain at designated depths from the surface under inclement weather.