Indigenous migrant workers (IMWs) have a high vulnerability to HIV and STDs due to poverty and marginalization. This study examined factors associated with sexual risk behavior (SRB) according to type of partner in transnational young male IMWs at a sugar cane agro-industrial complex in western Mexico. A total of 192 sexually active IMWs were recruited from four laborer shelters to participate in a sexual partner survey. The IMWs were interviewed about their sexual partners and practices over the last 12 months during which it emerged that they had had a total of 360 sexual partners. Multiple linear regression analyses were performed to identify factors related to SRB in 222 main (spouse, mistress and girlfriend) and 138 casual partners (colleague, friend, casual encounter and sex worker). Results showed a significantly higher SRB score with casual partners. For the main partner regression model, prior exposure to HIV- and STD-preventive information and sexual intercourse with higher employment status partners (formal workers vs. self-employed in informal activities and unemployed) were associated with lower SRB scores, but if the sexual relations occurred in Mexico (vs. the U.S.), the SRB scores increased. For the casual partner model, the practice of survival sex (sex in exchange for basic needs), sexual relations in Mexico (vs. the U.S.), and being a circular migrant (person traveling for temporary work to return home when the contract is over) were related to higher SRB scores. Findings support the implementation of preventive interventions using different messages depending on the type of partners, main or casual, within the labor migrant context.