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<p>Abstract</p> <p>Background</p> <p>A comprehensive malaria control intervention was initiated in February 2004 on Bioko Island, Equatorial Guinea. This manuscript reports on the continuous entomological monitoring of the indoor residual spray (IRS) programme during the first two years of its implementation.</p> <p>Methods</p> <p>Mosquitoes were captured daily using window traps at 16 sentinel sites and analysed for species identification, sporozoite rates and knockdown resistance <it>(kdr</it>) using polymerase chain reaction (PCR) to assess the efficacy of the vector control initiative from December 2003 to December 2005.</p> <p>Results</p> <p>A total of 2,807 and 10,293 <it>Anopheles funestus </it>and <it>Anopheles gambiae s.l. </it>respectively were captured throughout the study period. Both M and S molecular forms of <it>An. gambiae s.s. </it>and <it>Anopheles melas </it>were identified. Prior to the first round of IRS, sporozoite rates were 6.0, 8.3 and 4.0 for <it>An. gambiae s.s.</it>, <it>An. melas </it>and <it>An. funestus </it>respectively showing <it>An. melas </it>to be an important vector in areas in which it occurred. After the third spray round, no infective mosquitoes were identified. After the first spray round using a pyrethroid spray the number of <it>An. gambiae s.s. </it>were not reduced due to the presence of the <it>kdr </it>gene but <it>An funestus </it>and <it>An. melas </it>populations declined from 23.5 to 3.1 and 5.3 to 0.8 per trap per 100 nights respectively. After the introduction of a carbamate insecticide in the second round, <it>An. gambiae s.s. </it>reduced from 25.5 to 1.9 per trap per 100 nights and <it>An. funestus </it>and <it>An. melas </it>remained at very low levels. <it>Kdr </it>was found only in the M-form of <it>An. gambiae s.s. </it>with the highest frequency at Punta Europa (85%).</p> <p>Conclusion</p> <p>All three vectors that were responsible for malaria transmission before the start of the intervention were successfully controlled once an effective insecticide was used.</p> <p>Continuous entomological surveillance including resistance monitoring is of critical importance in any IRS based malaria vector control programme. This paper demonstrates that sufficient resources for such monitoring should be included in any proposal in order to avoid programme failures.</p>