The disruption of the endosperm, a tissue responsible for nourishing the embryo in the seeds of flowering plants, is a common occurrence in inviable hybrid seeds of closely related species. A key question is whether parental conflict plays a significant role in this type of reproductive isolation. To explore this question, we conducted reciprocal crosses between pairs of three species of monkeyflowers (Mimulus caespitosa, M. tilingii, and M. guttatus) and observed varying degrees of hybrid seed inviability, which we attributed to differences in species divergence in effective ploidy. A time series of seed development led us to identify parent-of-origin phenotypes that strongly indicate the role of parental conflict in shaping the evolution of the endosperm. Specifically, we discovered pronounced differences in the growth of the chalazal haustorium, a tissue within the endosperm that develops at the maternal-filial boundary, between reciprocal hybrid seeds formed from Mimulus species that differ in effective ploidy. These parent-of-origin effects suggest that the chalazal haustorium may act as a mediator of parental conflict, possibly by regulating the movement of sucrose from the maternal parent into the endosperm. Our findings imply that parental conflict in the endosperm may function as a driver for speciation by targeting critical developmental stages and regions essential for resource allocation and proper seed development.