Monitoring field conditions are the foundation of modern agricultural management in order to improve the efficiency of the data collection procedure. Thus, it is necessary that the Ecuadorian Agency of Quality Assurance in Agro-quality collects environmental data and environmental fluctuations in order to determinate the pattern of Tephritid fruit flies. One of the important areas of fruit production is Santa Elena, located in the western coast. The main objective of this study is to determine the monitoring of fruit flies and their relation with biotic and abiotic factors. The methodology applied was the slope, soil texture and climatological maps as well as 694 traps in a research area of 3,466 ha distributed in the central, northern, southern and western part of Santa Elena region analyzed with the principal factor analysis. The results indicated that the minimum–maximum temperature, relative humidity and rainfall were the major climatic factors influencing fly populations. The soil texture did not have any influence on the development stage of caterpillars. Trapping and rearing data indicated that the genus Ceratitis was common during the dry season and reached a peak at the end of the dry season. It attacked both early and mid-season agricultural production. On the other hand, Anastrepha fraterculus, A. oblique, A. serpentina, A. punensis, A. manihoti, A. chiclayae and A. pickeli which were also identified, are native species and were widely distributed. This highlights the priority of the management of fruit flies, which is the main limitation for the export of diverse fruits and vegetables produced in Ecuador.