Understanding disease vector composition is of priority in designing effective disease control programs. In integrated vector control management, understanding of disease vector species among species complexes simplifies priorities for effective control tools selection. This study identified members of the Anopheles funestus complex sampled in western Kenya from 2002 to 2011 from different breeding sites. Larval sampling was carried out using the standard dipper (350ml) in larval habitats in western Kenya highlands from January 2002 to December 2012. The morphologically identified An. funestus larvae were preserved in absolute ethanol for molecular identification using polymerase chain reaction (PCR). Among the 184 identified specimens of An. funestus sampled, only 76 specimens were clearly identified after DNA amplification and PCR. Among these, 25 (32.9%) were An. funestus s.s, 22 (28.9%) An. leesoni, 9 (11.8%) An. rivulorum and 20 (26.3%) were An. vaneedeni. None was identified as An. parensis. This study has demonstrated the existence of the siblings species of An. funestus complex in western Kenya highlands. However, there is need for further studies to evaluate the dynamics of the adults and sporozoite infectivity rates throughout the region based on these findings.