Even though there are data published on HPV epidemiology in Ecuador, the distribution of genotypes in Guayaquil, the largest city in the country, has not been previously determined in a study including including both, men and women. The present study aimed to determine the distribution of 37 HPV genotypes in genital samples from Ecuadorian men and women living in the city of Guayaquil. Genital samples included in daily diagnostic routine were analyzed by the 37 HPV GenoArray Diagnostic Kit (Hybribio® Ltd., Sheung Wan, Hong Kong). The relative frequency of detectable genotypes was determined. HPV relative frequency according to sample characteristics, including sex and age groups, was compared using c2 test. From the 800 samples (400 men and 400 women), 411 (51.38%) were positive for HPV DNA. The obtained frequency was higher among samples from men (253/400 or 63.25%) in comparison to samples from women (158/400 or 39.50%), with a p value <0.05. Samples from men showed a higher frequency of HPV genotypes 6, 16, 18 and 11, while among samples from women genotypes 39, 16, 6 and 58 were the most frequent. Considering male and female samples together, genotypes 6, 16, 39 and 11 presented the highest frequencies. HPV DNA was detected in half of the studied samples, with a higher frequency among samples from men. Genotype 39 was the most frequent among women, and ranked third when samples from men and women are analyzed together.