The primary difference is that Long Tail Pro is a big time saver over MS. With Long Tail Pro you are able to enter in multiple seed keywords at once (rather than just 1 with MS). So, instead of entering in 1 seed keyword, waiting five minutes, then going back and entering in one more; you can enter 5 seed keywords (for example), hit generate and then see all the keyword ideas at once!

Keyword Researcher is designed to search the Autocomplete databases of Google, YouTube, and even Amazon.com. That's a lot of keyword sources! As you probably know, if you're building an authority site, or if you would like to become a dominant player in your niche, then starting with a large database of keywords (that your customers are actually typing in) is a powerful marketing tool.

"I've used many keyword tools over the years and Keyword Researcher is up there amongst the most useful of them. Apart from being a great way to get ideas for content, as an AdWords consultant, I also use it to uncover words and phrases that my clients would not want to be bidding on (negative keywords). This is a real time saver for me and a budget enhancer for my clients! All in all, this is a great app and should be used by any professional search engine marketer."
To drive search engine traffic, whether through organic search or paid search advertisements, you need the right keywords, plus a process to expand your keyword lists over time. That’s where our free tool comes in. WordStream’s Free Keyword Tool gives you hundreds of relevant keyword results, plus additional, actionable information like competition level and estimated CPC, all for free!

You can filter your results by 24 business verticals, including Apparel, Arts & Entertainment, Autos & Vehicles, Beauty & Fitness, Books & Literature, Business & Industrial, Computers & Electronics, Finance & Banking, Food & Drink, Toys & Games, Health, Hobbies & Leisure, Home & Garden, Internet & Telecom, Jobs & Education, Law & Government, News Media & Publications, Family & Community, Occasions & Gifts, Pets & Animals, Real Estate, Retail & General Merchandise, Sports & Fitness, and Travel & Tourism.
This database was built using data from BEFORE Google required active ad accounts to get good keyword data & before they started blending data together for similar terms. Even if you set up an AdWords account and spend significant sums of money with them, they may require you to run your ad campaign for 3 or 4 months straight before they will show reasonably precise data instead of exceptionally broad data ranges.
Long Tail Pro is a keyword research tool that helps you quickly find low competition keywords for your website.  In particular, the tool is built for people doing SEO (search engine optimization) as opposed to people doing paid ads (Google Adwords PPC).  I'm sure there are some advertisers that use the tool for paid ad keyword research, but the tool was built for SEO keyword research.
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