Yellow is female, but a running gag of the manga is for her to disguise herself as a boy and for most people not to notice otherwise. Her disguise simply consists of putting a hat over her head to hide her long blonde ponytail. She first did this in the Yellow arc by the instruction of Green (or Blue in Japan), being ordered by her to keep her gender a secret at all costs unless it could be beneficial. Green also told her to do this to make it harder for others to track her, but even after the events of the Gold/Silver/Crystal arc she is still seen doing it (for some reason she didn't inform Red about what is the content of the hat, though Red knows about it at chapter 180) until the end of the Gold/Silver/Crystal arc. All later appearances she has appeared as a female and often without her hat.
Her overall design is that she has long yellow-blonde hair in a ponytail with a layered fringe at the front, and wears a straw sun hat most of the time, even when she is revealed to be a girl. She is also short for her age and slim, and wears a long sleeved black shirt under a yellow tunic dress that is edged with green, blue tights and purple ankle boots. Her eyes are a dark greenish yellow.
Yellow is mostly happy-go-lucky and quite brave. She also is shown to be fairly smart when she is fighting Lance. Yellow is kind-hearted and seems to be close with Pokémon.
Red, Green and Blue arc
She first appeared in volume three of the first arc though only with a minor cameo, where she was rescued by Red in Viridian Forest and later nursed him back to health after he defeated Giovanni and asked him if he can be the new gym leader of Viridian City, Red promised her he will take the role after he became stronger.
She appeared as the main protagonist sent out by Green to look for the missing Red, she hid her identity by wearing a hat given to her by Green. She later found out that the Elite Four were behind the reason why Red was missing and the chaos in the Kanto region. With Red's Pika and her other Pokémon, she was able to defeat Lance with the move called Megavolt.
She helped Gold, Silver and Crystal along with the other Pokédex Holders during this chapter. It is also in this chapter that Red finally knew that Yellow was a girl (because she had to remove her hat), which also surprised Gold and Crystal.
FireRed and LeafGreen arc
She appeared to help Silver find his Dad, though in the end, they turned into stone.
They were freed from they're stone state because of the help of Emerald, Ruby, Gold, Crystal, and Sapphire. The other Pokédex holders used Hydro Cannon, Blast Burn and Frenzy Plant. She stated that it was impossible to defeat Kyogre. Gold told Yellow that it was not impossible, and that's when Pika, Chuchu and Pichu used Volt Tackle to win in the battle against Kyogre in the Emerald Arc. Later, they are surprised when Red said that why won't they hold a match and each and every Pokédex Holder will join, it is known that Emerald won it.
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Yellow is also known as the Healer because she heals Pokémon. She gets these powers from being born in the Viridan Forest. Only two other people in the manga, Lance and Giovanni, have been shown to have similar powers due to also being born there. She can also read memories of Pokémon and understand them.
She can use some telekinesis, shown when she controlled the Poké Ball on the Fishing Rod. She can also make her Pokémon's levels skyrocket into the 80's in desperate situations.
There's also clues that Yellow had a crush on Red as seen in the last chapter of the Yellow arc where she woke up in Red's Gyarados and Red (didn't know Yellow true identity) jokingly said that they should live together since Pika really likes Yellow, at that time Yellow saw a red thread that connects Red's little finger and hers. Another clues is that at the end of G/S/C arc where she looks worried when Red got a call from Misty (who also probably had feelings for Red).
Despite being introduced as the fourth Pokédex owner, she is officially the ninth (Between Ruby and Emerald).
Yellow, along with Emerald, are the only manga protagonists to not appear in the anime or games, or be based on anime/game characters.