Recently diverged population in the early stages of speciation offer an opportunity to understand mechanisms of isolation and their relative contribution. Drosophila willistoni is a tropical species with broad distribution from Argentina to the southern United States, including the Caribbean islands. We have recently documented a postzygotic barrier between Central America, North America, and the northern Caribbean islands (D. w. willistoni) from South American and the southern Caribbean islands (D. w. winge). Here we identify premating isolation between strains regardless of their subspecies status, with the effect being dependent on environment. We find no evidence of postmating prezygotic isolation and proceed to characterize hybrid male sterility among the subspecies. Sterile male hybrids transfer an ejaculate that is devoid of sperm but causes elongation and expansion of the female uterus. In sterile male hybrids, bulging of the seminal vesicle appears to impede the movement of the sperm towards the sperm pump, where sperm normally mixes with accessory glands products. Our results highlight a unique form of hybrid male sterility in Drosophila that is driven by a mechanical impediment to transfer sperm rather than by an abnormality of the sperm itself. Interestingly, this form of sterility is reminiscent of a form of infertility (azoospermia) that is caused by lack of sperm in the semen due to blockages that impede the sperm from reaching the ejaculate.