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Coccidiosis in chickens is a parasitic disease of economic importance for the poultry industry. In Ecuador, there is limited information regarding the prevalence of <i>Eimeria</i> spp. on commercial broiler farms. Therefore, a total of 155 poultry farms in the provinces of Pichincha and Santo Domingo de los Tsáchilas were surveyed. The analysis of fresh fecal samples was conducted to determine the parasitic load of six of the seven chicken <i>Eimeria</i> species (excluding <i>E. mitis</i>) through multiplex PCR. Additionally, an epidemiological survey was performed to assess the risk factors associated with the infection using a multivariable logistic regression model. All samples tested positive for the presence of <i>Eimeria</i> spp., despite the farmers having implemented prophylactic measures, and no clinical coccidiosis cases were recorded. The parasitic load varied between 25 and 69,900 oocyst per gram. The species prevalence was as follows: <i>Eimeria</i> spp. 100%, <i>E. maxima</i> 80.4%, <i>E. acervulina</i> 70.6%, <i>E. praecox</i> 55.4%, <i>E. tenella</i> 53.6%, <i>E. necatrix</i> 52.2%, and <i>E. brunetti</i> 30.8%. The main species combination was <i>E. cervuline</i>, <i>E. maxima</i>, <i>E. necatrix</i>, and <i>E. praecox</i> (23.90%), followed by <i>E. tenella</i>, as a unique species (10.69%), and then E. <i>acervulina</i>, <i>E. maxima</i>, and <i>E. praecox</i> (8.81%). It was observed that farms operated by independent producers had a higher amount of <i>Eimeria</i> spp. and higher probability of the presence of <i>E. brunetti</i>, <i>E. necatrix</i>, <i>E. praecox</i>, and <i>E. tenella</i>. Poultry houses located below 1300 m above sea level were associated with a higher parasitic load and the presence of <i>E. brunetti</i>. Birds younger than 35 days of age and from open-sided poultry houses (with rudimentary environmental control) had a higher probability of presenting <i>E. maxima</i>. Drinking water from wells increased the risk of <i>E. praecox</i> presence. Research aimed at designing control strategies to improve health management on poultry farms in the region would help minimize the impact of coccidiosis.