X-Men '97 positively portrays LGBTQ+ themes through its allegorical depiction of mutants as marginalized groups, emphasizing discrimination, identity, and found family. The character Morph is presented as non-binary, using shapeshifting to reflect gender fluidity, aligning with the show's focus on self-acceptance and community strength. The narrative affirms queer experiences without using explicit modern terminology.

X-Men '97 portrays trans and non-binary identities primarily through Morph, reimagined as non-binary, and through Storm's gender-bending redesign. The series emphasizes authenticity, aims for representation, and explores themes of identity and self-acceptance, reflecting and affirming gender diversity within its universe.

The show features Rogue, a female character with super strength, who repeatedly engages in and wins close-quarters physical fights against multiple male opponents, including human adversaries and male-coded robots, throughout the series.

In X-Men '97, the character Morph, originally established as male in source material, is portrayed as nonbinary. This change aligns with the definition of a gender swap.

The series portrays Nightcrawler's devout Catholicism with respect and nuance, depicting his faith as a source of compassion, inclusive ministry, and moral reflection for himself and other mutants.

Magneto's Jewish identity as a Holocaust survivor is central, with the narrative using his experiences to powerfully condemn antisemitism, religious intolerance, and the historical suffering of Jewish people.