Samus Aran usually wears a bulky suit of armor that hides her appearance. The people who played the original Metroid game would only discover that Samus was a female if they managed to complete the game in under three hours, which was no easy feat, so there are many people who played the game at the time who completed it while under the impression that Samus was male. The instruction booklet that came with Metroid also referred to Samus as male.
It seems that the secret of Samus' gender was so well-kept that it managed to fool some of the people who were making official merchandise for the game, as was the case with Victory Techniques for Metroid.
Victory Techniques for Metroid was a Japan exclusive strategy guide that functioned as a manga, with the story of the game being told in comic book form. The most notable aspect of Victory Techniques for Metroid is that it depicts Samus as a male (though he never removes his armor) and he is even seen partying with a few bikini babes at the start of the book.
The other notable aspect of Victory Techniques for Metroid is that it features cameos and references to the other Nintendo games of the time. These references include Samus playing the original The Legend of Zelda game and letting Link be defeated by Octoroks and mistaking the pipes that the aliens come out of for one of the Warp Pipes from Super Mario Bros, which involved a cameo from Mario. Victory Techniques for Metroid was released in 1986, which means that it beat out the first Super Smash Bros. game by thirteen years in terms of bringing the classic Nintendo characters together.
Victory Techniques for Metroid was a quirky manga that showed a comedic version of Samus as he completed his mission on the planet Zebes. The fact that Samus was male in the manga and love to party with bikini-clad anime girls might seem like sacrilege to some, but it's due to this misunderstanding of the character that this amusing manga/strategy guide combo became known to the world.
Victory Techniques for Metroid was never released outside of Japan, but an unofficial scanlation of the book can be found on the Metroid Database website here.