The New Civil Rights Movement explains how the new rule works:

Because Indiana marriage license forms have a space for “male applicant” and “female applicant”, any same-sex couple filling out the form would automatically violate the law. The harsh penalties Indiana lawmakers have approved make it difficult for protest movements like the Campaign for Southern Equality’s ” We Do” Campaign, which encourages same-sex couples to apply for marriage licenses as a protest in states that prohibit same-sex marriages.

More: The Backlash Begins: Indiana Makes Same-Sex Marriage a Felony Punishable by Prison