BackgroundCutaneous Leishmaniasis (CL) affects up to 5.000 people in Ecuador each year.L. guyanensisandL. braziliensisare the most common of the eight CL-causingLeishmaniaspecies. Earlier CL research concentrated on the easily accessible Pacific region. This study aims to describe theLeishmaniaspecies in Pacific and Amazon ecoregions, to analyze regional differences in CL patient clinical presentation, and to identify determinants of health-seeking delay.MethodsAll cases in this cross-sectional study were diagnosed using smear slide microscopy, PCR, or both. Cytochrome B gene sequencing was used to identify the causativeLeishmaniaspecies in qPCR-positive samples.ResultsThis study included 245 patients, with 154 (63%) infected in the Pacific region and 91 (37%) infected in the Amazon. CausativeLeishmaniaspecies were identified in 135 patients (73% of qPCR positives).L. guyanensiswas identified in 76% (102/135) of the samples andL. braziliensisin 19% (26/135). The Pacific region had a low prevalence of 6% (5/89) ofL. braziliensis. For the first time, we reportL. guyanensisfrom the central Amazon,L. braziliensisfrom the northern Pacific, andL. lainsonifrom both the central Amazon and northern Pacific. Amazon cases had a longer median health-seeking delay in months (2.0, IQR 3.0) than Pacific cases (1.0, IQR 1.5). Prolonged health-seeking delay was associated with older age, Amerindian ethnicity, infection at lower altitudes, non-ulcerative lesions, and lesions on the lower limbs.ConclusionsIn the Pacific region, health-seeking delay is relatively short andL. braziliensisprevalence remains low. Limited access to health care and stigma might explain the prolonged health-seeking delay in the Amazon. We recommend larger studies on the distribution ofLeishmaniaspecies in Amazon CL cases and additional regional research into diagnostic test accuracy. Furthermore, the determinants of health-seeking delay in Ecuador should be investigated further.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-023-08377-8.