Purpose: Malaria transmission is one of the consequences of climate variability and change. The burden is greatest in the developing countries of the tropics especially Africa south of the Sahara. In Kenya, particularly the Lower Lake Victoria Basin (LLVB), it is blamed on the historical high rainfall, temperature and relative humidity. This study sought to determine spatiotemporal variation of malaria transmission in different altitudes of the LLVB, Kenya.
 Methodology: The study relied on data from routine malaria case transmission records archived by the Health Information System for ten years. Data for Kakamega, Kisumu and Migori Counties were obtained from the Kenya Health Information System (KHIS) through Sub-County Health Facilities. Pearson’s Product Moment Correlation Coefficient was used to correlate the suspected and confirmed transmission cases. ANOVA was used in testing the variability of transmission, Time Series to determine transmission characteristics while malaria case transmission tables and Tukeys Honest Significance Difference (HSD) were for testing the significance of the distribution of malaria.
 Findings: The suspected cases were found to have been overstated in Migori and Kakamega Counties. Malaria transmission varied by altitude, space and time during the study period. Trends increased in Kisumu and Kakamega Counties while it decreased in Migori County. Transmission depicted both endemic and epidictic characteristics in the study area.
 Unique Contribution to Theory, Policy and Practices: Health facilities in the LLVB, Kenya should be equipped with more modern laboratory equipment to improve confirmation of transmission so as to reduce suspicions. Since most of the observations confirmed the varying nature of malaria transmission in relation to altitude, the aspect of blanket assumption concerning malaria transmission in the LLVB, Kenya should be stopped. LLVB, Kenya should be zoned by altitudes for effective mitigation and eradication strategies. The reduction of malaria case transmission in Migori County was an indication of possible future eradication. Its cause should be investigated and inferred to other counties. More research is necessary to establish situations elsewhere for effective management and control of transmissions. The revelations and recommendations were expected to enhance malaria eradication in the LLVB, Kenya and subsequently promote the realization of Kenya’s vision 2030.
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